Miracle-dz/UniFAR-FTUs huggingface dataset:
Cardiac Catheterization in Assessment and Treatment of Kawasaki Disease in Children and Adolescents

Cardiac catheterization has become a promising tool to assess and treat coronary artery lesions in patients with Kawasaki disease. Significant coronary artery lesions can now be treated via transcatheter route even in small children. Further development and miniaturization of this technology will help to promote widespread use to the benefit of small children suffering from coronary artery disease. The role of diagnostic and interventional coronary artery procedures in children and adolescents are discussed in this article.
Using Convolutional Neural Networks to Support Insertion of New Concepts into SNOMED CT

Many major medical ontologies go through a regular (bi-annual, monthly, etc.) release cycle. A new release will contain corrections to the previous release, as well as genuinely new concepts that are the result of either user requests or new developments in the domain. New concepts need to be placed at the correct place in the ontology hierarchy. Traditionally, this is done by an expert modeling a new concept and running a classifier algorithm. We propose an alternative approach that is based on providing only the name of a new concept and using a Convolutional Neural Network-based machine learning method. We first tested this approach within one version of SNOMED CT and achieved an average 88.5% precision and an F1 score of 0.793. In comparing the July 2017 release with the January 2018 release, limiting ourselves to predicting one out of two or more parents, our average F1 score was 0.701.
Long-Term Whole Grain Wheat and Rye Intake Reflected by Adipose Tissue Alkylresorcinols and Breast Cancer: A Case-Cohort Study

Whole grain rye (WGR) and whole grain wheat (WGW) have been suggested to protect against the development of breast cancer. In this study, we estimated long-term intake of WGR and WGW, using both a food frequency questionnaire (FFQ) and alkylresorcinol concentrations in adipose tissue biopsies, in relation to the risk of developing invasive breast cancer in a case-cohort study (n = 414 in the case group, n = 933 in the subcohort group) on the Danish “Diet, Cancer and Health” cohort. The median follow-up time of the subcohort was 5.3 years. Total WGR and WGW intake estimated with FFQ or reflected by total alkylresorcinol concentration in adipose tissue was not significantly associated with risk of breast cancer. However, after adjustment for total WGR and WGW intake, women in the highest quartile of relative WGR intake, reflected by the alkylresorcinol C17:0/C21:0 ratio, had a higher risk of overall breast cancer and estrogen-receptor-positive (ER+) breast cancer than women in the lowest quartile of relative WGR intake, while the risk of estrogen-receptor-negative (ER-) breast cancer incidence was unaffected. Similar results were obtained with the FFQ data. Based on these data, further investigation of the role of specific grain types in reducing or increasing breast cancer risk, and their overall impact on health, is warranted.
Short photoperiod reduces the temperature sensitivity of leaf‐out in saplings of Fagus sylvatica but not in horse chestnut

Leaf phenology is one of the most reliable bioindicators of ongoing global warming in temperate and boreal zones because it is highly sensitive to temperature variation. A large number of studies have reported advanced spring leaf‐out due to global warming, yet the temperature sensitivity of leaf‐out has significantly decreased in temperate deciduous tree species over the past three decades. One of the possible mechanisms is that photoperiod is limiting further advance to protect the leaves against potential damaging frosts. However, the “photoperiod limitation” hypothesis remains poorly investigated and experimentally tested. Here, we conducted a photoperiod‐ and temperature‐manipulation experiment in climate chambers on two common deciduous species in Europe: Fagus sylvatica (European beech, a typically late flushing species) and Aesculus hippocastanum (horse chestnut, a typically early flushing species). In agreement with previous studies, we found that the warming significantly advanced the leaf‐out dates by 4.3 and 3.7 days/°C for beech and horse chestnut saplings, respectively. However, shorter photoperiod significantly reduced the temperature sensitivity of beech only (3.0 days/°C) by substantially increasing the heat requirement to avoid leafing‐out too early. Interestingly, the photoperiod limitation only occurs below a certain daylength (photoperiod threshold) when the warming increased above 4°C for beech trees. In contrast, for chestnut, no photoperiod threshold was found even when the ambient air temperature was warmed by 5°C. Given the species‐specific photoperiod effect on leaf phenology, the sequence of the leaf‐out timing among forest tree species may change under future climate warming conditions. Nonphotoperiodic species may benefit from warmer springs by starting the growing season earlier than photoperiodic sensitive species, modifying forest ecosystem structure and functions, but this photoperiod limitation needs to be further investigated experimentally in numerous species.
Feasibility and acceptance of the CaringGuidance web‐based, distress self‐management, psychoeducational program initiated within 12 weeks of breast cancer diagnosis

Limited clinical resources create barriers to quality management of cancer‐related distress. CaringGuidance After Breast Cancer Diagnosis is a web‐based, patient‐controlled, psychoeducational program of cognitive‐behavioral, coping and problem‐solving strategies aimed at early post‐diagnosis distress reduction without clinical resources. This study evaluated the feasibility of recruiting and retaining newly diagnosed women to 12 weeks of CaringGuidance and program acceptance.
The Family Resilience Inventory: A Culturally Grounded Measure of Current and Family-of-Origin Protective Processes in Native American Families.

The purpose of this article is to introduce the Family Resilience Inventory (FRI) and present findings on initial efforts to validate this measure. The FRI is designed to assess family resilience in one's current family and in one's family of origin, enabling the assessment of family protective factors across these generations. The development of the FRI was the result of many years of ethnographic research with Southeastern Native American tribes; yet, we believe that this scale is applicable to families of various backgrounds. Items for the FRI were derived directly from thematic analysis of qualitative data with 436 participants, resulting in two 20-item scales. Due to missing data, eight cases were removed from the 127 participants across two tribes, resulting in an analytic sample size of 119. Conceptually, the FRI is comprised of two factors or scales measuring distinct dimensions of family resilience (i.e., resilience in one's current family and resilience in one's family of origin). The results of the confirmatory factor analysis supported the hypothesized two-factor structure (X2 (644) = 814.14, p = . 03, X2 /df = 1.10, RMSEA = . 03, CFI = . 97, TLI = . 96). Both the subscales and the total FRI scale (α = .92) demonstrated excellent reliability. The results also provided preliminary evidence of convergent and discriminant validity. This measure fills a gap in the absence of community-based, culturally grounded, and empirical measures of family resilience. The examination of family resilience, which may occur across generations, is an exciting new contribution of the FRI.
New guidelines for DNA methylome studies regarding 5-hydroxymethylcytosine for understanding transcriptional regulation

Many DNA methylome profiling methods cannot distinguish between 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). Since 5mC typically acts as a repressive mark whereas 5hmC is an intermediate form during active demethylation, the inability to separate their signals could lead to incorrect interpretation of the data. Meanwhile, many analysis pipelines quantify methylation level by the count or ratio of methylated reads, but the proportion of discordant reads (PDR) has recently been proposed to be a better indicator of gene expression level. Is the amount of extra information contained in 5hmC signals and PDR worth the additional experimental and computational costs? Here we combine whole-genome bisulfite sequencing (WGBS) and oxidative WGBS (oxWGBS) data in normal human lung and liver tissues and their paired tumors to investigate the quantitative relationships between gene expression and signals of the two forms of DNA methylation at promoters, transcript bodies, and immediate downstream regions. We find that 5mC and 5hmC signals correlate with gene expression in the same direction in most samples, but considering both types of signals increases the accuracy of expression levels inferred from methylation data by a median of 18.2% as compared to having only standard WGBS data, showing that the two forms of methylation provide complementary information about gene expression. In addition, differential analysis between matched tumor and normal pairs is particularly affected by the superposition of 5mC and 5hmC signals in WGBS data, with at least 25-40% of the differentially methylated regions (DMRs) identified from 5mC signals not detected from WGBS data. We do not find PDR to be more informative about expression levels than ratio of methylated reads, and integrating the two types of methylation features only improves the accuracy of inferred expression levels by at most 9.8%. Our results also confirm previous finding that methylation signals at transcript bodies are more indicative of gene expression levels than promoter methylation signals, and further show that in addition to the first exon, methylation signals at the last exon and internal introns also contain non-redundant information about gene expression. Overall, our study provides concrete data for evaluating the cost effectiveness of some experimental and analysis options in the study of DNA methylation in normal and cancer samples.
Psychophysiological Indicators for Modeling User Experience in Interactive Digital Entertainment †

Analyses of user experience in the electronic entertainment industry currently rely on self-reporting methods, such as surveys, ratings, focus group interviews, etc. We argue that self-reporting alone carries inherent problems—mainly the misinterpretation and temporal delay during longer experiments—and therefore, should not be used as a sole metric. To tackle this problem, we propose the possibility of modeling consumer experience using psychophysiological measures and demonstrate how such models can be trained using machine learning methods. We use a machine learning approach to model user experience using real-time data produced by the autonomic nervous system and involuntary psychophysiological responses. Multiple psychophysiological measures, such as heart rate, electrodermal activity, and respiratory activity, have been used in combination with self-reporting to prepare training sets for machine learning algorithms. The training data was collected from 31 participants during hour-long experiment sessions, where they played multiple video-games. Afterwards, we trained and compared the results of four different machine learning models, out of which the best one produced ∼96% accuracy. The results suggest that psychophysiological measures can indeed be used to assess the enjoyment of digital entertainment consumers.
Efficient Fabrication of Polycaprolactone Scaffolds for Printing Hybrid Tissue-Engineered Constructs

Hybrid constructs represent substantial progress in tissue engineering (TE) towards producing implants of a clinically relevant size that recapitulate the structure and multicellular complexity of the native tissue. They are created by interlacing printed scaffolds, sacrificial materials, and cell-laden hydrogels. A suitable biomaterial is a polycaprolactone (PCL); however, due to the higher viscosity of this biopolymer, three-dimensional (3D) printing of PCL is slow, so reducing PCL print times remains a challenge. We investigated parameters, such as nozzle shape and size, carriage speed, and print temperature, to find a tradeoff that speeds up the creation of hybrid constructs of controlled porosity. We performed experiments with conical, cylindrical, and cylindrical shortened nozzles and numerical simulations to infer a more comprehensive understanding of PCL flow rate. We found that conical nozzles are advised as they exhibited the highest shear rate, which increased the flow rate. When working at a low carriage speed, conical nozzles of a small diameter tended to form-flatten filaments and became highly inefficient. However, raising the carriage speed revealed shortcomings because passing specific values created filaments with a heterogeneous diameter. Small nozzles produced scaffolds with thin strands but at long building times. Using large nozzles and a high carriage speed is recommended. Overall, we demonstrated that hybrid constructs with a clinically relevant size could be much more feasible to print when reaching a tradeoff between temperature, nozzle diameter, and speed.
Potential of Sentinel-1 Surface Soil Moisture Product for Detecting Heavy Rainfall in the South of France

The objective of this paper is to present an analysis of Sentinel-1 derived surface soil moisture maps (S1-SSM) produced with high spatial resolution (at plot scale) and a revisit time of six days for the Occitanie region located in the South of France as a function of precipitation data, in order to investigate the potential of S1-SSM maps for detecting heavy rainfalls. First, the correlation between S1-SSM maps and rainfall maps provided by the Global Precipitation Mission (GPM) was investigated. Then, we analyzed the effect of the S1-SSM temporal resolution on detecting heavy rainfall events and the impact of these events on S1-SSM values as a function of the number of days that separated the heavy rainfall and the S1 acquisition date (cumulative rainfall more than 60 mm in 24 hours or 80 mm in 48 hours). The results showed that the six-day temporal resolution of the S1-SSM map doesn’t always permit the detection of an extreme rainfall event, because confusion will appear between high S1-SSM values due to extreme rainfall events occurring six days before the acquisition of S1-SSM, and high S1-SSM values due to light rain a few hours before the acquisition of Sentinel-1 images. Moreover, the monitoring of extreme rain events using only soil moisture maps remains difficult, since many environmental parameters could affect the value of SSM, and synthetic aperture radar (SAR) doesn’t allow the estimation of very high soil moistures (higher than 35 vol.%).
Ecological and Evolutionary Processes Shaping Viral Genetic Diversity

The contemporary genomic diversity of viruses is a result of the continuous and dynamic interaction of past ecological and evolutionary processes. Thus, genome sequences of viruses can be a valuable source of information about these processes. In this review, we first describe the relevant processes shaping viral genomic variation, with a focus on the role of host–virus coevolution and its potential to give rise to eco-evolutionary feedback loops. We further give a brief overview of available methodology designed to extract information about these processes from genomic data. Short generation times and small genomes make viruses ideal model systems to study the joint effect of complex coevolutionary and eco-evolutionary interactions on genetic evolution. This complexity, together with the diverse array of lifetime and reproductive strategies in viruses ask for extensions of existing inference methods, for example by integrating multiple information sources. Such integration can broaden the applicability of genetic inference methods and thus further improve our understanding of the role viruses play in biological communities.
Cardioprotective and Vasodilatory Actions of Glucagon-Like Peptide 1 Receptor Are Mediated Through Both Glucagon-Like Peptide 1 Receptor–Dependent and –Independent Pathways

Background— The glucagon-like peptide 1 receptor (GLP-1R) is believed to mediate glucoregulatory and cardiovascular effects of the incretin hormone GLP-1(7-36) (GLP-1), which is rapidly degraded by dipeptidyl peptidase-4 (DPP-4) to GLP-1(9-36), a truncated metabolite generally thought to be inactive. Novel drugs for the treatment of diabetes include analogues of GLP-1 and inhibitors of DPP-4; however, the cardiovascular effects of distinct GLP-1 peptides have received limited attention. Methods and Results— Here, we show that endothelium and cardiac and vascular myocytes express a functional GLP-1R as GLP-1 administration increased glucose uptake, cAMP and cGMP release, left ventricular developed pressure, and coronary flow in isolated mouse hearts. GLP-1 also increased functional recovery and cardiomyocyte viability after ischemia-reperfusion injury of isolated hearts and dilated preconstricted arteries from wild-type mice. Unexpectedly, many of these actions of GLP-1 were preserved in Glp1r−/− mice. Furthermore, GLP-1(9-36) administration during reperfusion reduced ischemic damage after ischemia-reperfusion and increased cGMP release, vasodilatation, and coronary flow in wild-type and Glp1r−/− mice, with modest effects on glucose uptake. Studies using a DPP-4–resistant GLP-1R agonist and inhibitors of DPP-4 and nitric oxide synthase showed that the effects of GLP-1(7-36) were partly mediated by GLP-1(9-36) through a nitric oxide synthase–requiring mechanism that is independent of the known GLP-1R. Conclusions— These data describe cardioprotective actions of GLP-1(7-36) mediated through the known GLP-1R and novel cardiac and vascular actions of GLP-1(7-36) and its metabolite GLP-1(9-36) independent of the known GLP-1R. Our data suggest that the extent to which GLP-1 is metabolized to GLP-1(9-36) may have functional implications in the cardiovascular system.
First-Rank Symptoms in Methamphetamine Psychosis and Schizophrenia

Background: Methamphetamine psychosis (MAP) symptomatology has been described as indistinguishable from that of schizophrenia (SZ), yet research comparing these two disorders on specific psychotic symptoms such as schneiderian first-rank symptoms (FRS) is lacking. We aimed to determine and compare the occurrence and associations of FRS in patients diagnosed with MAP and with SZ. Sampling and Method: Data from SCID-I interviews performed on patients with either a diagnosis of SZ or MAP were compared. We calculated the prevalence of different FRS between MAP and SZ patients and used logistic regression to assess the association between FRS and diagnosis. Results: 102 patients were included in the study (MAP = 33, SZ = 69). Thought broadcasting occurred significantly more often in SZ (42%) than in MAP (24.2%) patients (adjusted OR = 3.02; 95% CI: 1.12-8.15; p = 0.028), while auditory hallucinations (voices conversing) were significantly higher in MAP (48.5%) than in SZ (20.3%) patients (adjusted OR = 0.27; 95% CI: 0.10-0.66; p = 0.004). However, there was no significant difference in the occurrence of one or more FRS in MAP and SZ, with most FRS showing overlap. Conclusions: We found that first-rank auditory hallucinations were more prevalent in MAP, whereas first-rank delusions of thought broadcasting were more prevalent in SZ. However, there was a substantial overlap in MAP and SZ for most FRS. This is consistent with the finding that FRS may have limited diagnostic specificity and that there is significant overlap in the symptoms of MAP and SZ. Future research into the neurobiology of delusions and hallucinations needs to take FRS into account.
Markedly Reduced Risk of Internal Malignancies in Patients With Vitiligo: A Nationwide Population-Based Cohort Study.

PURPOSE Recent studies indicated that the autoimmunity of vitiligo exerts effects on cells other than melanocytes, which confer reduced risks of both melanoma and nonmelanoma skin cancers in patients with vitiligo. However, the risk of internal malignancy in patients with vitiligo has not been elucidated. PATIENTS AND METHODS We conducted a population-based retrospective cohort study using data from the Korean National Health Insurance claims database obtained from January 2007 to December 2016. All patients age 20 years or older with vitiligo who had at least two contacts with a physician from 2009 to 2016, during which a principal diagnosis was made, were identified (vitiligo group). Controls were randomly selected (two per patient with vitiligo) after frequency matching with the vitiligo group for age and sex during the same period (control group). RESULTS A total of 101,078 patients with vitiligo and 202,156 controls without vitiligo were included. The incidence rates of internal malignancies were 612.9 and 708.9 per 100,000 person-years in the vitiligo and control groups, respectively. Patients with vitiligo showed a significantly reduced risk of overall internal malignancies (hazard ratio [HR], 0.86; 95% CI, 0.82 to 0.89; P < .001) compared with controls without vitiligo after adjustments for age, sex, and comorbidities. With regard to organ-specific malignancies, patients with vitiligo showed a remarkably decreased risk of cancer in the colon and rectum (HR, 0.62; 95% CI, 0.55 to 0.69; P < .001), ovary (HR, 0.62; 95% CI, 0.46 to 0.83; P < .001), and lung (HR, 0.75; 95% CI, 0.65 to 0.86; P < .001). CONCLUSION Vitiligo was associated with a reduced risk of overall internal malignancies. These findings suggest that autoimmune diseases, including vitiligo, may provide immune surveillance for the development of cancer beyond the targeted organ.
Logistic Classification Models for pH-Permeability Profile: Predicting Permeability Classes for the Biopharmaceutical Classification System

Permeability is used to describe and evaluate the absorption of drug substances in the human gastrointestinal tract (GIT). Permeability is largely dependent on fluctuating pH that causes the ionization of drug substances and also influences regional absorption in the GIT. Therefore, classification models that characterize permeability at wide ranges of pH were derived in the current study. For this, drug substances were described with six data series that were measured with a parallel artificial membrane permeability assay (PAMPA), including a permeability profile at four pH values (3, 5, 7.4, and 9), and the highest and intrinsic membrane permeability. Logistic regression classification models were developed and compared by using two distinct sets of descriptors: (1) a hydrophobicity descriptor, the logarithm of the octanol-water partition (logPow) or distribution (logD) coefficient and (2) theoretical molecular descriptors. In both cases, models have good classification and descriptive capabilities for the training set (accuracy: 0.76-0.91). Triple validation with three sets of drug substances shows good prediction capability for all models: validation set (accuracy: 0.73-0.91), external validation set (accuracy: 0.72-0.9), and the permeability classes of FDA reference drugs for the biopharmaceutical classification system (BCS) (accuracy: 0.72-0.88). The identification of BCS permeability classes was further improved with decision trees that consolidated predictions from models with each descriptor type. These decision trees have higher confidence and accuracy (0.91 for theoretical molecular descriptors and 0.81 for hydrophobicity descriptors) than the individual models in assigning drug substances into BCS permeability classes. A detailed analysis of classification models and related decision trees suggests that they are suitable for predicting classes of permeability for passively transported drug substances, including specifically within the BCS framework. All developed models are available at the QsarDB repository ( http://dx.doi.org/10.15152/QDB.206 ).