Miracle-dz/UniFAR-FTUs huggingface dataset:
Demographics and Clinical Profiles of Patients Visiting a Free Clinic in Miami, Florida

Background: Although the ranks of the uninsured in the United States have decreased in recent years, some states still lack Medicaid expansion programs, leaving many Americans, especially the indigent and homeless, without adequate healthcare coverage. Free-for-care clinics are oftentimes the last safety net for these vulnerable populations. Because these clinics have limited funding, a thorough understanding of the patients they serve is necessary to effectively direct their resources. The objective of the present study is to investigate the characteristics and clinical profiles of patients utilizing a free clinic in Miami, Florida. Methods: Aggregate EMR data reflecting consecutive adult patient visits to the Miami Rescue Mission Clinic in Miami, Florida between January 1st, 2018 to March 15th, 2019 (n = 846) were reviewed for sociodemographic characteristics and chronic disease prevalence. Prevalence rates were compared by sex and to county estimates from the Florida Behavioral Risk Factor Surveillance System. Results: The most common conditions were mental health (19.3%), circulatory system (14.7%), and musculoskeletal system disorders (13.9%). Males had a greater prevalence of depression (difference = 6.6%; 95% CI [1.5 to 10.7%]; χ2 = 6.2; p = 0.013) and overall mental illness (22.0 vs. 10.4%, difference = 11.6%; 95% CI [5.7 to 16.4%]; χ2 = 13.2; p = 0.0003) compared to females, and male sex was identified as an independent risk factor for mental illness on multivariate logistic regression analysis (OR = 2.8; 95% CI [1.7 to 4.7]; p < 0.001). There was also a higher prevalence of depression (difference = 6.41%; 95% CI [2.1 to 10.2%]; χ2 = 8.0; p = 0.0047) and HIV (difference = 1.4%; 95% CI [0.3 to 3.0%]; χ2 = 7.3; p = 0.007) in male patients compared to county estimates. Rates of hypertension, diabetes, elevated cholesterol, asthma, and COPD were lower in the clinic population compared to the surrounding county. Conclusion: There is an acute need for mental health services in this population. The lowered prevalence of other chronic conditions is due to underdiagnosis and loss to follow-up. Such analyses are important in guiding policy decisions for meeting the health needs of vulnerable, at risk populations.
Climate Driven Changes in Timing, Composition and Magnitude of the Baltic Sea Phytoplankton Spring Bloom

Spring phytoplankton blooms contribute a substantial part to annual production, support pelagic and benthic secondary production and influence biogeochemical cycles in many temperate aquatic systems. Understanding environmental effects on spring bloom dynamics is important for predicting future climate responses and for managing aquatic systems. We analyzed long-term phytoplankton data from one coastal and one offshore station in the Baltic Sea to uncover trends in timing, composition and size of the spring bloom and its correlations to environmental variables. There was a general trend of earlier phytoplankton blooms by 1–2 weeks over the last 20 years, associated with more sunshine and less windy conditions. High water temperatures were associated with earlier blooms of diatoms and dinoflagellates that dominate the spring bloom, and decreased diatom bloom magnitude. Overall bloom timing, however, was buffered by a temperature and ice related shift in composition from early blooming diatoms to later blooming dinoflagellates and the autotrophic ciliate Mesodinium rubrum. Such counteracting responses to climate change highlight the importance of both general and taxon-specific investigations. We hypothesize that the predicted earlier blooms of diatoms and dinoflagellates as a response to the expected temperature increase in the Baltic Sea might also be counteracted by more clouds and stronger winds. A shift from early blooming and fast sedimenting diatoms to later blooming groups of dinoflagellates and M. rubrum at higher temperatures during the spring period is expected to increase energy transfers to pelagic secondary production and decrease spring bloom inputs to the benthic system, resulting in lower benthic production and reduced oxygen consumption.
Keap1/Nrf2 Signaling: A New Player in Thyroid Pathophysiology and Thyroid Cancer

The Keap1/Nrf2 pathway is a key mediator of general redox and tissue-specific homeostasis. It also exerts a dual role in cancer, by preventing cell transformation of normal cells but promoting aggressiveness, and drug resistance of malignant ones. Although Nrf2 is well-studied in other tissues, its roles in the thyroid gland are only recently emerging. This review focuses on the involvement of Keap1/Nrf2 signaling in thyroid physiology, and pathophysiology in general, and particularly in thyroid cancer. Studies in mice and cultured follicular cells have shown that, under physiological conditions, Nrf2 coordinates antioxidant defenses, directly increases thyroglobulin production and inhibits its iodination. Increased Nrf2 pathway activation has been reported in two independent families with multinodular goiters due to germline loss-of-function mutations in KEAP1. Nrf2 pathway activation has also been documented in papillary thyroid carcinoma (PTC), due to somatic mutations, or epigenetic modifications in KEAP1, or other pathway components. In PTC, such Nrf2-activating KEAP1 mutations have been associated with tumor aggressiveness. Furthermore, polymorphisms in the prototypical Nrf2 target genes NQO1 and NQO2 have been associated with extra-thyroidal extension and metastasis. More recently, mutations in the Nrf2 pathway have also been found in Hürthle-cell (oncocytic) thyroid carcinoma. Finally, in in vitro, and in vivo models of poorly-differentiated, and undifferentiated (anaplastic) thyroid carcinoma, Nrf2 activation has been associated with resistance to experimental molecularly-targeted therapy. Thus, Keap1/Nrf2 signaling is involved in both benign and malignant thyroid conditions, where it might serve as a prognostic marker or therapeutic target.
Disarming Pseudomonas aeruginosa Virulence by the Inhibitory Action of 1,10-Phenanthroline-5,6-Dione-Based Compounds: Elastase B (LasB) as a Chemotherapeutic Target

Elastase B (lasB) is a multifunctional metalloenzyme secreted by the gram-negative pathogen Pseudomonas aeruginosa, and this enzyme orchestrates several physiopathological events during bacteria-host interplays. LasB is considered to be a potential target for the development of an innovative chemotherapeutic approach, especially against multidrug-resistant strains. Recently, our group showed that 1,10-phenanthroline-5,6-dione (phendione), [Ag(phendione)2]ClO4 (Ag-phendione) and [Cu(phendione)3](ClO4)2.4H2O (Cu-phendione) had anti-P. aeruginosa action against both planktonic- and biofilm-growing cells. In the present work, we have evaluated the effects of these compounds on the (i) interaction with the lasB active site using in silico approaches, (ii) lasB proteolytic activity by using a specific fluorogenic peptide substrate, (iii) lasB gene expression by real time-polymerase chain reaction, (iv) lasB protein secretion by immunoblotting, (v) ability to block the damages induced by lasB on a monolayer of lung epithelial cells, and (vi) survivability of Galleria mellonella larvae after being challenged with purified lasB and lasB-rich bacterial secretions. Molecular docking analyses revealed that phendione and its Ag+ and Cu2+ complexes were able to interact with the amino acids forming the active site of lasB, particularly Cu-phendione which exhibited the most favorable interaction energy parameters. Additionally, the test compounds were effective inhibitors of lasB activity, blocking the in vitro cleavage of the peptide substrate, aminobenzyl-Ala-Gly-Leu-Ala-p-nitrobenzylamide, with Cu-phendione having the best inhibitory action (Ki = 90 nM). Treating living bacteria with a sub-inhibitory concentration (½ × MIC value) of the test compounds caused a significant reduction in the expression of the lasB gene as well as its mature protein production/secretion. Further, Ag-phendione and Cu-phendione offered protective action for lung epithelial cells, reducing the A549 monolayer damage by approximately 32 and 42%, respectively. Interestingly, Cu-phendione mitigated the toxic effect of both purified lasB molecules and lasB-containing bacterial secretions in the in vivo model, increasing the survival time of G. mellonella larvae. Collectively, these data reinforce the concept of lasB being a veritable therapeutic target and phendione-based compounds (mainly Cu-phendione) being prospective anti-virulence drugs against P. aeruginosa.
Monensin Sensitive 1 Regulates Dendritic Arborization in Drosophila by Modulating Endocytic Flux

Monensin Sensitive 1 (Mon1) is a component of the Mon1:Ccz1 complex that mediates Rab5 to Rab7 conversion in eukaryotic cells by serving as a guanine nucleotide exchange factor for Rab7 during vesicular trafficking. We find that Mon1 activity modulates the complexity of Class IV dendritic arborization (da) neurons during larval development. Loss of Mon1 function leads to an increase in arborization and complexity, while increased expression, leads to reduced arborization. The ability of Mon1 to influence dendritic development is possibly a function of its interactions with Rab family GTPases that are central players in vesicular trafficking. Earlier, these GTPases, specifically Rab1, Rab5, Rab10, and Rab11 have been shown to regulate dendritic arborization. We have conducted genetic epistasis experiments, by modulating the activity of Rab5, Rab7, and Rab11 in da neurons, in Mon1 mutants, and demonstrate that the ability of Mon1 to regulate arborization is possibly due to its effect on the recycling pathway. Dendritic branching is critical for proper connectivity and physiological function of the neuron. An understanding of regulatory elements, such as Mon1, as demonstrated in our study, is essential to understand neuronal function.
On the role of discourse relations in persuasive texts

This paper investigates the use of explicitly signalled discourse relations in persuasive texts. We present a corpus study where we control for speaker and topic and show that the distribution of different discourse connectives varies considerably across different discourse settings. While this variation can be explained by genre differences, we also observe variation regarding the distribution of discourse relations across different settings. This variation, however, cannot be easily explained by genre differences. We argue that the differences regarding the use of discourse relations reflects different strategies of persuasion and that these might be due to audience design.
Defining What Empirically Works Best: Dynamic Generation of Meta-Analysis for Computer Science Education

In an effort to evaluate computer science education using more modern, automated data science techniques, we consider Hattie's work in Visible Learning then define a comprehensive framework to provide the capability to automatically generate a quantitative meta-analysis using predefined moderators (e.g., age, grade, etc.) with data derived from multiple individual research studies. To define the initial criteria, we developed a list of critical questions that the framework must address, including what moderators are most important to include, how to address homogeneity across various studies, how to define categories of influencing factors, and how to compute summary effect size. This initial framework describes how the meta-analysis is derived from effect sizes that are calculated based on each mean and standard deviation reported in experimental and quasi-experimental studies. Since the goal of this foundational research is to create an auto-generated meta-analysis tool, we define a basic user experience that would allow users to select moderators and predefined levels of heterogeneity (such as "include only random control group studies" or "include studies reported in journal articles") for inclusion in the meta-analysis. We conducted a feasibility study of the framework using data (number of participants, mean, standard deviation) collected from 21 data samples curated from eight computer science education articles with a primary and secondary focus across ten venues (2012-2018). We consider what we learned conducting the study, including the need for full system transparency, issues related to data integrity, and issues related to defining and selecting appropriate formulas for differing sets of data.
Towards a General Abstract Meaning Representation Corpus for Brazilian Portuguese

Abstract Meaning Representation (AMR) is a recent and prominent semantic representation with good acceptance and several applications in the Natural Language Processing area. For English, there is a large annotated corpus (with approximately 39K sentences) that supports the research with the representation. However, to the best of our knowledge, there is only one restricted corpus for Portuguese, which contains 1,527 sentences. In this context, this paper presents an effort to build a general purpose AMR-annotated corpus for Brazilian Portuguese by translating and adapting AMR English guidelines. Our results show that such approach is feasible, but there are some challenging phenomena to solve. More than this, efforts are necessary to increase the coverage of the corresponding lexical resource that supports the annotation.
Research This! Questions that Computing Educators Most Want Computing Education Researchers to Answer

The goal of many computing education researchers is to improve how computing is taught and learned. To do that, researchers must engage with teachers, coaches, and mentors who design instructional materials and deliver lessons. However researchers may not be investigating problems that are directly of interest or utility to practitioners, and thus may not deliver results that are as impactful as possible in their contexts. To find out what research most interests today's practitioners, we conducted a two-stage survey. The first stage gathered questions that practitioners want researchers to investigate, and the second stage ranked these questions in terms of importance. We found that today's practitioners are more interested in student behavior, student understanding, and pedagogy than in languages and tools, curriculum, and inclusivity, and that there is little overlap between the questions ranked as highly interesting by researchers and those ranked highly by practitioners. Our results indicate that researchers need to better communicate why the questions they are pursuing are important, look for opportunities to collaborate with those who teach but have little direct connection with research, and examine the relevance of their research questions to practitioners.
Annotating and analyzing the interactions between meaning relations

Pairs of sentences, phrases, or other text pieces can hold semantic relations such as paraphrasing, textual entailment, contradiction, specificity, and semantic similarity. These relations are usually studied in isolation and no dataset exists where they can be compared empirically. Here we present a corpus annotated with these relations and the analysis of these results. The corpus contains 520 sentence pairs, annotated with these relations. We measure the annotation reliability of each individual relation and we examine their interactions and correlations. Among the unexpected results revealed by our analysis is that the traditionally considered direct relationship between paraphrasing and bi-directional entailment does not hold in our data.
Supporting Rapid Product Changes through Emotional Tracking

Agile principles have led to short development cycles with rapid changes in requirements, especially for mobile apps. The success of apps highly depends on their acceptance by the users. However, testing user acceptance is usually costly and timeconsuming. This imposes a conflict between quality and agility. As current verification and validation methods for requirements do not always fit the demands for volatile requirements, we propose the idea of emotional tracking. In this positional paper, we present how the vision of tracking emotions shown by users while interacting with an app might be realized by using 3D sensing cameras in smartphones. We propose a plan for the technical and organizational process of emotional tracking on the user's device and the backend and an experiment setup to link muscular positions to emotions, to preserve user privacy. With emotional tracking, we provide a new method for verification and validation of software requirements. Our method can be used in parallel to development activities and combines quantitative usage data with users' feelings and emotions to get a fast and holistic idea of an app's user acceptance.
A systematic review of the international prevalence of BRCA mutation in breast cancer

Abstract A systematic review was conducted, summarizing international BRCA 1 or 2 (BRCA1/2) mutation prevalence in breast cancer. Databases (eg, Medline and Embase; N=7) and conferences were searched (January 2012 to December 2017). From 17,872 records, 70 studies were included. In 58 large (N>100) studies, BRCA1/2 mutation prevalence varied widely from 1.8% (Spain) in sporadic breast cancer to 36.9% (United States) in estrogen receptor/progesterone receptor low+ (1–9% on immunohistochemistry/human epidermal growth factor receptor 2–negative [HER2-]) breast cancer. In 2 large studies unselected for family history, ethnicity, sex, or age and no/unclear selection by breast cancer stage or hormone receptor (HR) status, germline BRCA (gBRCA) mutation prevalence was 2.9% (Italy) to 3.0% (South Korea). In the 4 large unselected triple-negative breast cancer studies, gBRCA mutation prevalence varied from 9.3% (Australia) to 15.4% (United States). gBRCA mutation prevalence in 1 large unselected HR positive/HER2- early breast cancer study was 5% (United States). In 2 large unselected metastatic breast cancer studies, gBRCA mutation prevalence was 2.7% (France) and 4.3% (Germany). Locally advanced breast cancer studies were small and not in unselected populations. Poor reporting of gBRCA status and basis of selection implies a need for further large well-reported BRCA mutation prevalence studies in breast cancer.
Predictors of inguinal lymph node metastasis in penile cancer patients: a meta-analysis of retrospective studies

Purpose Inguinal lymph node metastasis (LNM) is one of the most significant prognostic factors for patients with penile cancer. This study aimed to identify potential predictors of inguinal LNM. Patients and methods A comprehensive search of the PubMed, Embase, and Cochrane Library databases for studies that reported predictors of inguinal LNM in penile cancer was performed. Finally, we selected 42 eligible studies with 4,802 patients. Accumulative analyses of odds ratios (ORs) and corresponding 95% confidence intervals (CIs) were performed. All analyses were performed by using Review Manager software version 5.3. Results Among the 4,802 patients, 1,706 (36%) were diagnosed with inguinal LNM. Predictors of LNM included two categories: tumor-associated biomarkers and invasive clinicopathologic characteristics. Biomarker-specific predictors: the program death ligand 1 (PD-L1) overexpression (OR=2.55, p=0.002), higher neutrophil-to-lymphocyte ratio (NLR) (OR=4.22, p=0.010), higher C-reactive protein (CRP) (OR=4.78, p<0.001), squamous cell carcinoma antigen (SCC-Ag) overexpression (OR=8.52, p<0.001), P53 protein overexpression (OR=3.57, p<0.001). Clinicopathological predictors: positive clinical lymph node (cN+) (OR=5.86, p<0.001), high-risk histopathological subtype (OR=14.63, p<0.001) and intermediate-risk subtype (OR=3.37, p<0.001), vertical growth pattern (OR=1.97, p=0.020), higher stage (AJCC: OR=3.66, p<0.001; UICC: OR=2.43, p<0.001), higher tumor grade (OR=3.37, p<0.001), tumor size (>3 cm) (OR=2.00, p=0.002), LVI (OR=3.37, p<0.001), invasion depth (>5 mm) (OR=2.58, p=0.002), nerve invasion (OR=2.84, p<0.001), corpora cavernosum invasion (OR=2.22, p<0.001), corpus spongiosum invasion (OR=1.73, p=0.002) and urethra invasion (OR=1.81, p=0.030). Conclusion Current meta-analysis conclusively identified valuable predictors of inguinal LNM for patients with penile cancer. However, high-quality studies are warranted to further validate our conclusions. The intrinsic link between these predictors needs to be further investigated to create an accurate mathematical prediction model for LNM.
Histological type of focal cortical dysplasia is associated with the risk of postsurgical seizure in children and adolescents

Aim Focal cortical dysplasia (FCD) is a common cause of refractory epilepsy in children and adolescents. Epilepsy surgery is a treatment option for FCD. This study aimed to investigate the relationship between postsurgical outcomes and FCD types according to the International League Against Epilepsy (ILAE) classification and assess prognostic factors in pediatric and adolescent epilepsy surgery. Methods We retrospectively analyzed 92 children and adolescents with a proven pathological diagnosis of FCD who underwent resective surgery at our epilepsy center between August 2012 and September 2015. The patients were followed up for at least 1 year to evaluate the surgical outcomes, and a multivariable regression analysis was performed to identify risk factors of seizure relapse. Results After surgery, 53.3% of the patients were completely seizure-free during the entire follow-up period. The FCD types, incomplete resection of the epileptic cortex, and use of intracranial electrode were independent risk factors of seizure recurrence. The patients with FCD type II had relatively favorable surgical outcomes compared to the patients with FCD type I. The difference in the postoperative outcome between patients with FCD types III and I was not significant. Conclusion There is a significant association between FCD types and surgical outcomes in children and adolescents with epilepsy. These findings provide guidance for the optimization of surgical strategies.
miR-21: a promising biomarker for the early detection of colon cancer

Purpose The aim of this study was to compare the expression of miR-21 gene in stages II-IV of formalin-fixed paraffin-embedded (FFPE) tissue in patients with colon cancer and introduce miR-21 as a potential molecular marker for detection of colon cancer in the early stages. Introduction Currently, identification of key molecules involved in the pathogenesis of cancer is one of the areas under consideration. miRNAs, are small RNAs which have been identified in many cancers. In this study, we investigated the expression of miR-21 in three pathologic stages in patients with colon cancer in the north of Iran. Patients and methods A total of 40 FFPE samples were obtained from patients with stages II, III, and IV from hospitals in Mazandaran and Golestan provinces. After extraction of RNA, treatment with DNase I and cDNA synthesis was performed and miR-21 expression was assessed by qPCR. Then, the data were analyzed using statistical software R (3.4.3). Results The expression of miR-21 in stage II was significantly different from stage IV. However, no significant difference was observed between the other stages. In stage II, the level of miR-21 expression was higher in men than women. Moreover, in the second pathological stage, miR-21 expression was reduced in patients with adjacent lymphoid tissue engagement. In addition, the expression of miR-21 in grade I was significantly higher than grade II. Conclusion The results of this study suggest that miR-21 can be a diagnostic marker for early stages of colon cancer, especially in men. It can also be considered as a good candidate for targeted treatment of colon cancer in the early stages of the disease. Furthermore, for the first time, we suggested that miR-21 can be a good molecular marker for classification of the stages of colon cancer.