Miracle-dz/UniFAR-FTUs huggingface dataset:
Expanding the Secondary Use of Prostate Cancer Real World Data: Automated Classifiers for Clinical and Pathological Stage

Background Explicit documentation of stage is an endorsed quality metric by the National Quality Forum. Clinical and pathological cancer staging is inconsistently recorded within clinical narratives but can be derived from text in the Electronic Health Record (EHR). To address this need, we developed a Natural Language Processing (NLP) solution for extraction of clinical and pathological TNM stages from the clinical notes in prostate cancer patients. Methods Data for patients diagnosed with prostate cancer between 2010 and 2018 were collected from a tertiary care academic healthcare system's EHR records in the United States. This system is linked to the California Cancer Registry, and contains data on diagnosis, histology, cancer stage, treatment and outcomes. A randomly selected sample of patients were manually annotated for stage to establish the ground truth for training and validating the NLP methods. For each patient, a vector representation of clinical text (written in English) was used to train a machine learning model alongside a rule-based model and compared with the ground truth. Results A total of 5,461 prostate cancer patients were identified in the clinical data warehouse and over 30% were missing stage information. Thirty-three to thirty-six percent of patients were missing a clinical stage and the models accurately imputed the stage in 21–32% of cases. Twenty-one percent had a missing pathological stage and using NLP 71% of missing T stages and 56% of missing N stages were imputed. For both clinical and pathological T and N stages, the rule-based NLP approach out-performed the ML approach with a minimum F1 score of 0.71 and 0.40, respectively. For clinical M stage the ML approach out-performed the rule-based model with a minimum F1 score of 0.79 and 0.88, respectively. Conclusions We developed an NLP pipeline to successfully extract clinical and pathological staging information from clinical narratives. Our results can serve as a proof of concept for using NLP to augment clinical and pathological stage reporting in cancer registries and EHRs to enhance the secondary use of these data.
Connecting the Dots of Social Robot Design From Interviews With Robot Creators

Despite promises about the near-term potential of social robots to share our daily lives, they remain unable to form autonomous, lasting, and engaging relationships with humans. Many companies are deploying social robots into the consumer and commercial market; however, both the companies and their products are relatively short lived for many reasons. For example, current social robots succeed in interacting with humans only within controlled environments, such as research labs, and for short time periods since longer interactions tend to provoke user disengagement. We interviewed 13 roboticists from robot manufacturing companies and research labs to delve deeper into the design process for social robots and unearth the many challenges robot creators face. Our research questions were: 1) What are the different design processes for creating social robots? 2) How are users involved in the design of social robots? 3) How are teams of robot creators constituted? Our qualitative investigation showed that varied design practices are applied when creating social robots but no consensus exists about an optimal or standard one. Results revealed that users have different degrees of involvement in the robot creation process, from no involvement to being a central part of robot development. Results also uncovered the need for multidisciplinary and international teams to work together to create robots. Drawing upon these insights, we identified implications for the field of Human-Robot Interaction that can shape the creation of best practices for social robot design.
The Lower Limit of Reference of Urinary Albumin/Creatinine Ratio and the Risk of Chronic Kidney Disease Progression in Patients With Type 2 Diabetes Mellitus

A urine albumin/creatinine ratio (UACR) <30 mg/g is considered to be normal, while increased risk of incident hypertension and cardiovascular disease mortality in subjects with high normal UACR level had been observed. However, a mild elevated but normal UACR level was associated with the risk of initiating chronic kidney disease (CKD) is uncertain. We investigated whether higher normal UACR is associated with the risk of developing CKD. A total of 4821 subjects with type 2 diabetes mellitus (T2DM), an estimated glomerular filtration rate >60 ml/min/1.73 m2 and UACR <30 mg/g enrolled in a diabetes disease management program between 2006 and 2020 were studied. The optimal cutoff point for baseline UACR as a predictor for progression to CKD according to the 2012 KDIGO definition was calculated using receiving operating characteristic curve analysis. After a mean of 4.9 years follow-up, the CKD risk progression increased in parallel with the quartiles of baseline UACR <30 mg/g (p for trend <0.0001). UACR cutoff points of 8.44 mg/g overall, 10.59 mg/g in males and 8.15 mg/g in females were associated with the risk of CKD progression. In multivariate Cox regression analysis, the hazard ratios for the association between UACR (>8.44 mg/g, >10.9 mg/g, >8.15 mg/g in overall, male, and female patients, respectively) and the risk of CKD progression were significant. This study demonstrated that a cutoff UACR value of >10 mg/g could significantly predict the cumulative incidence and progression of CKD in patients with T2DM.
Editorial: Recent Advances in Micro-Nanostructured Optoelectronic Devices

Optoelectronic devices, including lasers, light-emitting diodes (LED), optical detectors and solar cells, have gained substantial attention in scientific research and been widely used in military and national economy fields such as laser detection and measurement, display and solid-state lighting, optical communications and environmental monitoring, and renewable energy sources (Bonaccorso et al., 2010; Lopez-Sanchez et al., 2013; Cao and Yan, 2021; Ye et al., 2021; Mao et al., 2021). The performance of optoelectronic devices needs to be continuously optimized towards high efficiency, small size, and low power consumption to meet the increasing demand of consumers. However, further improvement in performance remains a daunting challenge due to limited light extraction or absorption in conventional device architectures. Inspired by the organisms in nature, a growing number of researchers have demonstrated that micronanostructures could attribute unique optical, electrical, and mechanical properties to optoelectronic devices thus serving as one of the most promising solutions to this problem (Bi et al., 2013; Feng et al., 2017; Fusella et al., 2020; Linic et al., 2021). By designing and optimizing the construction in optoelectronic devices, the various micro-nanostructures can be acquired to realize corresponding efficient light manipulation effect such as enhancing light scattering and reducing light reflection, utilizing resonant plasmonic structures to improve light extraction or light absorption, adopting specific resonator geometries to achieve optical feedback, using photonic crystal to guide light propagation path and designing optical metasurfaces to control radiation properties directly at the source level (Choi et al., 2019; Joo et al., 2020; Liu et al., 2020; Zhou et al., 2020; Fu et al., 2021). To present these inspiring developments, we launched a Research Topic in Frontiers in Chemistry entitled “Recent Advances in Micro-Nanostructured Optoelectronic Devices. ” This Research Topic covers fabrication, light management mechanisms of micro-nanostructures in optoelectronic devices, and their emerging applications in display and lighting, solar energy harvesting, telecommunication, light sensing and detection, and other fields, including seven minireviews and three original research articles contributed from 51 researchers. The controllable fabrication of micro-nanostructures is a crucial condition to construct efficient micro-nanostructured optoelectronic devices. With the emergence of various kinds of micronanostructures manufacturing technologies, laser fabrication technologies can be used to fabricate micro-nanostructures by the interaction between lasers and materials, which show high efficiency, high precision, and low thermal effect, proving to be a competitive manufacturingmethod. Edited and reviewed by: Baiquan Liu, Sun Yat-sen University, China
Healthcare Provider Perspectives on Digital and Interprofessional Medication Management in Chronically Ill Older Adults of Turkish Descent in Germany: A Qualitative Structuring Content Analysis

Medication management for chronically ill older adults with a history of migration can be associated with specific challenges, for instance language barriers. This study examined healthcare provider perspectives on interprofessional cooperation and digital medication management tools as approaches for increasing medication safety for chronically ill older adults of Turkish descent in Germany. Semi-structured interviews were conducted with 11 healthcare providers, including general practitioners, pharmacists, a geriatric consultant, a hospital social worker, and an expert on digitalization in nursing care. The interviews were analyzed by means of qualitative structuring content analysis. This article presents selected results of the analysis relating to medication management, barriers to optimal medication management, interprofessional cooperation, and digital tools. Compliance was perceived to be high among chronically ill older adults of Turkish descent and the involvement of family members in medication management was rated positively by respondents. Barriers to medication management were identified in relation to health literacy and language barriers, systemic problems such as short appointments and generic substitution, and racism on behalf of healthcare providers. Additionally, the respondents highlighted structural barriers to interprofessional communication in the German healthcare system. Furthermore, two technology acceptance models presented in this article to illustrate the respondents' perspectives on a) a digital application for medication management to be used by chronically ill older adults of Turkish descent and b) a digital tool for interprofessional communication. The discussion highlights the implications of the results for medication management within the German healthcare system.
Sandfly Fever Viruses Attenuate the Type I Interferon Response by Targeting the Phosphorylation of JAK-STAT Components

Sandfly fever viruses are emerging Phleboviruses typically causing mild febrile illness. Some strains, however, can cause severe and occasionally fatal neuro-invasive disease. Like most viruses, Phleboviruses have devised various strategies to inhibit the type I interferon (IFN) response to support a productive infection. Still, most of the strategies identified so far focus on inhibiting the sensing arm of the IFN response. In contrast, the effect of sandfly virus infection on signaling from the IFN receptor is less characterized. Therefore, we tested the effect of sandfly fever virus Naples (SFNV) and Sicily (SFSV) infection on IFN signaling. We found that infection with either of these viruses inhibits signaling from the IFN receptor by inhibiting STAT1 phosphorylation and nuclear localization. We show that the viral nonstructural protein NSs mediates these effects, but only NSs from SFNV was found to interact with STAT1 directly. Thus, we tested the upstream IFN signaling components and found that Janus kinase 1 (Jak1) phosphorylation is also impaired by infection. Furthermore, the NSs proteins from both viruses directly interacted with Jak1. Last, we show that IFN inhibition by SFNV and SFSV is most likely downstream of the IFN receptor at the Jak1 level. Overall, our results reveal the multiple strategies used by these related viruses to overcome host defenses.
Construction of a Prognostic Model for KIRC and Identification of Drugs Sensitive to Therapies - A Comprehensive Biological Analysis Based on m6A-Related LncRNAs

As one of the common malignancies in the urinary system, kidney cancer has been receiving explorations with respect to its pathogenesis, treatment and prognosis due to its high morbidity, high mortality and low drug efficiency. Such epigenetic modifications for RNA molecules as N6-methyladenosine (m6A) usher in another perspective for the research on tumor mechanisms, and an increasing number of biological processes and prognostic markers have been revealed. In this study, the transcriptome data, clinical data and mutation spectrum data of KIRC in the TCGA database were adopted to construct an m6A-related lncRNA prognostic model. Besides, the predictive ability of this model for clinical prognosis was evaluated, and some compounds sensitive to therapies for KIRC were screened. The findings of this study demonstrate that this effective and stable model has certain clinical application value.
Trends on Microalgae-Fungi Consortia Research: An Alternative for Biofuel Production?

The utilization of microalgae and fungi on an industrial scale is a challenge for researchers. Based on the question “how fungi have contributed to microalgae research? ,” we verified the scientific trends on microalgae-fungi consortia focused on biofuels production by searching for articles on the Web of Science and Scopus databases through the terms “microalgae*” or phytoplankton and “fung*. ” We found 1,452 articles published between 1950 and 2020; since 2006, the publication numbers have increased rapidly. The articles were published in 12 languages, but most were written in English (96.3%). Among 72 countries, China (360 articles), USA (344), and Germany (155) led the publication rank. Among the 10 most-prolific authors, 8 were Chinese, like 5 of the most-productive institutions, whereas the National Cheng Kung University was on the top of the list. The sources that published the most on the subject were: Bioresource Technology (96), PLoS ONE (28), and Science of the Total Environment (26). The keyword analysis emphasized the magnitude of applications in microalgae-fungi consortia research. Confirming this research question, biofuels appeared as a research trend, especially biodiesel, biogas, and related terms like lipid, lipid accumulation, anaerobic digestion, and biogas upgrading. For 70 years, articles have been published, where China and the United States seem to dominate the research scenario, and biodiesel is the main biofuel derived from this consortium. However, microalgae-based biofuel biorefinery is still a bottleneck on an industrial scale. Recent environmental challenges, such as greenhouse gas mitigation, can be a promising field for that microalgae-fungi application.
Risk Factors for Cardiac Complications in Patients With Pheochromocytoma and Paraganglioma: A Retrospective Single-Center Study

Background Catecholamine excess arising from pheochromocytomas and paragangliomas (PPGLs) can cause a wide spectrum of cardiac manifestations. Although there are reviews of reported cases, these reviews lack detailed data, which makes it impossible to perform an accurate analysis. In this study, we conducted a comprehensive analysis of cardiovascular complications (CCs), including PPGL-related myocardial injury, cardiogenic shock, and arrhythmias requiring antiarrhythmic therapy, in a large cohort of patients with PPGL. Methods We retrospectively analyzed the clinical data of consecutive patients with PPGL admitted between January 2018 and June 2020. The prevalence and the characteristics of patients with CCs were investigated. Moreover, comparisons were made between patients with and without CCs. Results Compared with the non-CC group, the percentage of men was significantly lower (14/41 vs.92/175, 34.1% vs. 52.6%, p = 0.034) and the proportion of patients with paroxysmal hypertension was significantly higher (13/41 vs.29/173, 31.7% vs.16.8%, p = 0.03) in the CC group. More patients showed excessive sweating (19/41 vs 64/175, 46.3% vs. 24.0%, p = 0.004) and PPGL crisis (7/41 vs. 10/175, 17.1% vs.5.7%, p=0.035) in the CC group. In terms of laboratory findings, higher white blood cell [7.36 (6.49, 20.23) vs. 5.95 (5.1, 6.97)×109/L, p<0.001] and platelet [339.28 ± 108.54 vs. 250.66 ± 70.83(×109/L), p = 0.021] counts were more common in the CC group. There was also a higher prevalence of combination-producing PPGL in the CC group (13/24 vs.20/149, 54.2% vs.13.4%, p<0.001). However, the tumor size, invasive behavior on histology, and hemorrhage or necrosis on histology did not differ between the two groups. Platelet count [odds ratio (OR): 1.009; 95% confidence interval (CI) 1.001–1.016; p=0.023] and combination-secreting PPGL (OR: 5.009; 95% CI 1.365–18.38; p=0.015) are independent risk factors for CCs in patients with PPGL. Conclusions In patients with PPGL, even in the absence of signs and symptoms of CCs, a work up of cardiology should be strongly considered. Importantly, if patients with PPGLs have higher platelet counts and the combination-secreting pattern, they are more likely to have CCs. Thus, a careful cardiac evaluation should be performed.
A Major Downregulation of Circulating microRNAs in Zika Acutely Infected Patients: Potential Implications in Innate and Adaptive Immune Response Signaling Pathways

Zika virus (ZIKV) is an arbovirus mainly transmitted by mosquitos of the genus Aedes. The first cases of ZIKV infection in South America occurred in Brazil in 2015. The infection in humans causes diverse symptoms from asymptomatic to a syndrome-like dengue infection with fever, arthralgia, and myalgia. Furthermore, ZIKV infection during pregnancy is associated with fetal microcephaly and neurological disorders. The identification of host molecular mechanisms responsible for the modulation of different signaling pathways in response to ZIKV is the first step to finding potential biomarkers and therapeutic targets and understanding disease outcomes. In the last decade, it has been shown that microRNAs (miRNAs) are important post-transcriptional regulators involved in virtually all cellular processes. miRNAs present in body fluids can not only serve as key biomarkers for diagnostics and prognosis of human disorders but also contribute to cellular signaling offering new insights into pathological mechanisms. Here, we describe for the first time ZIKV-induced changes in miRNA plasma levels in patients during the acute and recovery phases of infection. We observed that during ZIKV acute infection, among the dysregulated miRNAs (DMs), the majority is with decreased levels when compared to convalescent and control patients. We used systems biology tools to build and highlight biological interactions between miRNAs and their multiple direct and indirect target molecules. Among the 24 DMs identified in ZIKV + patients, miR-146, miR-125a-5p, miR-30-5p, and miR-142-3p were related to signaling pathways modulated during infection and immune response. The results presented here are an effort to open new vistas for the key roles of miRNAs during ZIKV infection.
Changes in Periodic Limb Movements of Sleep After the Use of Continuous Positive Airway Pressure Therapy: A Meta-Analysis

Background Both obstructive sleep apnea (OSA) and periodic limb movements of sleep (PLMS) are common in the sleep laboratory. The severity of OSA can be improved by using continuous positive airway pressure (CPAP). However, increasing evidence has shown an elevated periodic limb movement index (PLMI) in patients with OSA who use CPAP, although the pathophysiology is still unknown. This meta-analysis aimed to investigate changes in PLMS after using CPAP and the potential pathophysiology of these changes. Methods Clinical trials in adult humans investigating the comorbidity between PLMS and CPAP were identified and analyzed using random-effects model meta-analysis. Results This meta-analysis included 14 studies comprising 2,938 patients with OSA. The PLMI was significantly increased after using CPAP with a difference in means of 1.894 (95% confidence interval = 0.651–3.138, p = 0.003). Subgroup analysis showed that CPAP was only significantly associated with an increase in PLMI in the patients without PLMS at baseline (p = 0.045) and in those with a baseline body-mass index <30 kg/m2 (p = 0.045). The use of CPAP, apnea-hypopnea index, and arousal index were positively correlated with changes in PLMI. Conclusion These characteristics may serve as qualitative predictive indicators of changes in PLMI after CPAP usage. Further analysis of the quantitative relationships between PLMI and the predictive indicators may be warranted. Trial Registration PROSPERO (registration number: CRD42021252635).
Results of the verification of the statistical distribution model of microseismicity emission characteristics

The paper presents the results of research aimed at verifying the hypothesis that the Weibull distribution is an appropriate statistical distribution model of microseismicity emission characteristics, namely: energy of phenomena and inter-event time. It is understood that the emission under consideration is induced by the natural rock mass fracturing. Because the recorded emission contain noise, therefore, it is subjected to an appropriate filtering. The study has been conducted using the method of statistical verification of null hypothesis that the Weibull distribution fits the empirical cumulative distribution function. As the model describing the cumulative distribution function is given in an analytical form, its verification may be performed using the Kolmogorov-Smirnov goodness-of-fit test. Interpretations by means of probabilistic methods require specifying the correct model describing the statistical distribution of data. Because in these methods measurement data are not used directly, but their statistical distributions, e.g., in the method based on the hazard analysis, or in that that uses maximum value statistics.
Editorial: Metabolic Flexibility

of Nutrition, Diabetes and Metabolism, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile, National Center for Scientific Research (CNRS), Pluridisciplinary Institute Hubert Curien (IPHC), University of Strasbourg, Strasbourg, France, Division of Endocrinology, Metabolism and Diabetes, Anschutz Health & Wellness Center, University of Colorado, Aurora, CO, United States, Univ-Lyon, CarMeN Laboratory, Inserm, Inrae, Université Claude Bernard Lyon-1, Lyon, France, 6 Institute of Metabolic and Cardiovascular Diseases, Team MetaDiab, Inserm/Paul Sabatier University, Toulouse, France, Centre de Recherche En Nutrition Humaine Rhône-Alpes, Univ-Lyon, CarMeN Laboratory, Hospices
Immunosensor of Nitrofuran Antibiotics and Their Metabolites in Animal-Derived Foods: A Review

Nitrofuran antibiotics have been widely used in the prevention and treatment of animal diseases due to the bactericidal effect. However, the residual and accumulation of their metabolites in vivo can pose serious health hazards to both humans and animals. Although their usage in feeding and process of food-derived animals have been banned in many countries, their metabolic residues are still frequently detected in materials and products of animal-derived food. Many sensitive and effective detection methods have been developed to deal with the problem. In this work, we summarized various immunological methods for the detection of four nitrofuran metabolites based on different types of detection principles and signal molecules. Furthermore, the development trend of detection technology in animal-derived food is prospected.