Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical Acronym/Abbreviation Normalization using a Hybrid Approach

A unique characteristic of clinical text is the pervasive use of acronyms and abbreviations, which are often ambiguous. The ShARe/CLEF eHealth Evaluation Lab organized three shared tasks on clinical natural language processing (NLP) and information retrieval (IR) in 2013 and one of them was to normalize acronyms/abbreviations to UMLS concept unique identifiers (CUIs). This paper describes a hybrid system, which combines different Word Sense Disambiguation (WSD) methods and existing knowledge bases to normalize and encode clinical abbreviations. Our system achieved the best accuracy of 0.719 on the independent test set, which was ranked first in the challenge.
Inhibition of sarcolemmal FAT/CD36 by sulfo-N-succinimidyl oleate rapidly corrects metabolism and restores function in the diabetic heart following hypoxia/reoxygenation

Aims The type 2 diabetic heart oxidizes more fat and less glucose, which can impair metabolic flexibility and function. Increased sarcolemmal fatty acid translocase (FAT/CD36) imports more fatty acid into the diabetic myocardium, feeding increased fatty acid oxidation and elevated lipid deposition. Unlike other metabolic modulators that target mitochondrial fatty acid oxidation, we proposed that pharmacologically inhibiting fatty acid uptake, as the primary step in the pathway, would provide an alternative mechanism to rebalance metabolism and prevent lipid accumulation following hypoxic stress. Methods and results Hearts from type 2 diabetic and control male Wistar rats were perfused in normoxia, hypoxia and reoxygenation, with the FAT/CD36 inhibitor sulfo-N-succinimidyl oleate (SSO) infused 4 min before hypoxia. SSO infusion into diabetic hearts decreased the fatty acid oxidation rate by 29% and myocardial triglyceride concentration by 48% compared with untreated diabetic hearts, restoring fatty acid metabolism to control levels following hypoxia-reoxygenation. SSO infusion increased the glycolytic rate by 46% in diabetic hearts during hypoxia, increased pyruvate dehydrogenase activity by 53% and decreased lactate efflux rate by 56% compared with untreated diabetic hearts during reoxygenation. In addition, SSO treatment of diabetic hearts increased intermediates within the second span of the Krebs cycle, namely fumarate, oxaloacetate, and the FAD total pool. The cardiac dysfunction in diabetic hearts following decreased oxygen availability was prevented by SSO-infusion prior to the hypoxic stress. Infusing SSO into diabetic hearts increased rate pressure product by 60% during hypoxia and by 32% following reoxygenation, restoring function to control levels. Conclusions Diabetic hearts have limited metabolic flexibility and cardiac dysfunction when stressed, which can be rapidly rectified by reducing fatty acid uptake with the FAT/CD36 inhibitor, SSO. This novel therapeutic approach not only reduces fat oxidation but also lipotoxicity, by targeting the primary step in the fatty acid metabolism pathway.
Opiate Antagonists Do Not Interfere With the Clinical Benefits of Stimulants in ADHD: A Double-Blind, Placebo-Controlled Trial of the Mixed Opioid Receptor Antagonist Naltrexone.

OBJECTIVE Methylphenidate activates μ-opioid receptors, which are linked to euphoria. μ-Opioid antagonists, such as naltrexone, may attenuate the euphoric effects of stimulants, thereby minimizing their abuse potential. This study assessed whether the combination of naltrexone with methylphenidate is well-tolerated while preserving the clinical benefits of stimulants in subjects with attention-deficit/hyperactivity disorder (ADHD). METHODS We conducted a 6-week, double-blind, placebo-controlled, randomized clinical trial of naltrexone in adults with DSM-IV ADHD receiving open treatment with a long-acting formulation of methylphenidate from January 2013 to July 2015. Spheroidal Oral Drug Absorption System (SODAS) methylphenidate was administered twice daily, was titrated to approximately 1 mg/kg/d over 3 weeks, and was continued for 3 additional weeks depending on response and adverse effects. Subjects were adults with ADHD preselected for having experienced euphoria with a test dose of immediate-release methylphenidate. The primary outcome measure was the Adult ADHD Investigator Symptom Report Scale (AISRS). RESULTS Thirty-seven subjects who experienced stimulant-induced (mild) euphoria at a baseline visit were started in the open trial of SODAS methylphenidate and randomly assigned to naltrexone 50 mg or placebo. Thirty-one subjects completed the study through week 3, and 25 completed through week 6. Throughout 6 weeks of blinded naltrexone and open methylphenidate treatment, the coadministration of naltrexone with methylphenidate did not interfere with the clinical effectiveness of methylphenidate for ADHD symptoms. Additionally, the combination of naltrexone and methylphenidate did not produce an increase in adverse events compared with methylphenidate alone. CONCLUSIONS Our findings provide support for the concept of combining opioid receptor antagonists with stimulants to provide an effective stimulant formulation with less abuse potential. TRIAL REGISTRATION ClinicalTrials.gov identifier: NCT01673594​.
Self‐assembling peptide matrix for treatment of dentin hypersensitivity: A randomized controlled clinical trial

BACKGROUND Patient-reported dentin hypersensitivity [DHS] pain is a common finding linked with periodontal disease. This pilot clinical study investigates a novel therapeutic regimen using self-assembling peptide matrix [SAPM] gel (test) compared with use of an 8% arginine and calcium carbonate [ACC] toothpaste (control) for treatment of DHS. METHODS A total of 50 patients with history of supportive periodontal therapy were enrolled in this prospective, randomized monocentric clinical study, of which 45 (test: n = 22; control: n = 23) fulfilled all the study visits. Test group patients performed ex-office application of SAPM gel over 1 week, while control group patients performed ex-office application of ACC toothpaste over 90 days. DHS was assessed in office by Visual Analog Scale [VAS], and patient's perception of pain relief was evaluated by questionnaire. In support of the clinical data, scanning electron microscopy images were recorded to investigate tubule occlusion of both control and test product. RESULTS Both SAPM and ACC significantly reduced DHS in patients throughout the study, with the patient questionnaire indicating higher patient satisfaction at the earlier time points for the test group. CONCLUSIONS Both SAPM gel and ACC toothpaste were successful in providing relief from DHS and showed similar outcomes on VAS and verbal response scale (VRS) throughout the study period of 90 days. The new therapeutic regimen using SAPM resulted in higher patient satisfaction at day 7, as indicated by the patient questionnaire and the higher number of pain-free patients at day 7 and day 90. This is a pilot study describing a novel therapy for DHS.
Illness perception ratings of high-risk newborns by mothers and clinicians: relationship to illness severity and maternal stress.

OBJECTIVE Patients' views of illness are often thought to differ from those of medical staff, although this is rarely assessed. This study examined the correspondence between mothers' and clinicians' perceptions of the same high-risk newborns, as well as with an objective measure of illness severity. We also investigated how mothers' perceptions were related to reported stress. METHODS Mothers of 99 high-risk infants admitted to either a neonatal intensive care or neonatal high dependency unit, which offers specialized but not intensive care, completed illness perception ratings of their baby's condition as well as perceived stress 3 to 5 days following admission. At the same time, a standardized measure of neonatal illness severity was calculated and the baby's primary neonatologist completed illness perceptions ratings. RESULTS Unlike clinician ratings, mothers' illness perceptions were not significantly correlated with illness severity. Mothers generally rated babies in both units as sicker and having a more serious illness than did neonatologists. Whereas clinicians, compared with mothers, rated babies in intensive care as having an illness that would affect their life more and last for a longer time. Mothers rated medical treatment to be significantly more helpful than did clinicians, particularly for babies admitted to the high dependency unit. Mothers' stress was significantly associated with illness perceptions but unrelated to illness severity. CONCLUSIONS Significant differences exist in the perceptions of illness severity, helpfulness of treatment, and the long-term effects of the baby's illness between parents and clinicians and this may lead to misunderstandings and misinterpretations in communication.
Quality Antibiotics in Agroecosystems : stAte of the science speciAl

The presence of antibiotic drug residues, antibiotic resistant bacteria, and antibiotic resistance genes in agroecosystems has become a significant area of research in recent years and is a growing public health concern. While antibiotics are used in both human medicine and agricultural practices, the majority of their use occurs in animal production where historically they have been used for growth promotion, in addition to the prevention and treatment of disease. The widespread use of antibiotics and the application of animal wastes to agricultural lands play major roles in the introduction of antibiotic-related contamination into the environment. Overt toxicity in organisms directly exposed to antibiotics in agroecosystems is typically not a major concern because environmental concentrations are generally lower than therapeutic doses. However, the impacts of introducing antibiotic contaminants into the environment are unknown, and concerns have been raised about the health of humans, animals, and ecosystems. Despite increased research focused on the occurrence and fate of antibiotics and antibiotic resistance over the past decade, standard methods and practices for analyzing environmental samples are limited and future research needs are becoming evident. To highlight and address these issues in detail, this special collection of papers was developed with a framework of five core review papers that address the (i) overall state of science of antibiotics and antibiotic resistance in agroecosystems using a causal model, (ii) chemical analysis of antibiotics found in the environment, (iii) need for background and baseline data for studies of antibiotic resistance in agroecosystems with a decision-making tool to assist in designing research studies, as well as (iv) cultureand (v) molecular-based methods for analyzing antibiotic resistance in the environment. With a focus on the core review papers, this introduction summarizes the current state of science for analyzing antibiotics and antibiotic resistance in agroecosystems, discusses current knowledge gaps, and develops future research priorities. This introduction also contains a glossary of terms used in the core reivew papers of this special section. The purpose of the glossary is to provide a common terminology that clearly characterizes the concepts shared throughout the narratives of each review paper. Antibiotics in Agroecosystems: Introduction to the Special Section
NRAS mutations in cutaneous T cell lymphoma (CTCL) sensitize tumors towards treatment with the multikinase inhibitor Sorafenib

Therapy of cutaneous T cell lymphoma (CTCL) is complicated by a distinct resistance of the malignant T cells towards apoptosis that can be caused by NRAS mutations in late-stage patients. These mutations correlate with decreased overall survival, but sensitize the respective CTCL cells towards MEK-inhibition-induced apoptosis which represents a promising novel therapeutic target in CTCL. Here, we show that the multi-kinase inhibitor Sorafenib induces apoptosis in NRAS-mutated CTCL cells. CTCL cell lines and to a minor extent primary T cells from Sézary patients without NRAS mutations are also affected by Sorafenib-induced apoptosis suggesting a sensitizing role of NRAS mutations for Sorafenib-induced apoptosis. When combining Sorafenib with the established CTCL medication Vorinostat we detected an increase in cell death sensitivity in CTCL cells. The combination treatment acted synergistically in apoptosis induction in both non-mutant and mutant CTCL cells. Mechanistically, this synergistic apoptosis induction by Sorafenib and Vorinostat is based on the downregulation of the anti-apoptotic protein Mcl-1, but not of other Bcl-2 family members. Taken together, these findings suggest that Sorafenib in combination with Vorinostat represents a novel therapeutic approach for the treatment of CTCL patients.
Two-photon calcium imaging during fictive navigation in virtual environments

A full understanding of nervous system function requires recording from large populations of neurons during naturalistic behaviors. Here we enable paralyzed larval zebrafish to fictively navigate two-dimensional virtual environments while we record optically from many neurons with two-photon imaging. Electrical recordings from motor nerves in the tail are decoded into intended forward swims and turns, which are used to update a virtual environment displayed underneath the fish. Several behavioral features—such as turning responses to whole-field motion and dark avoidance—are well-replicated in this virtual setting. We readily observed neuronal populations in the hindbrain with laterally selective responses that correlated with right or left optomotor behavior. We also observed neurons in the habenula, pallium, and midbrain with response properties specific to environmental features. Beyond single-cell correlations, the classification of network activity in such virtual settings promises to reveal principles of brainwide neural dynamics during behavior.
Topical Review: Adherence Interventions for Youth on Gluten-Free Diets

Objective To summarize gluten-free diet (GFD) nonadherence risk factors, nonadherence rates, and current intervention research within an integrative framework and to develop a research agenda for the development and implementation of evidence-based GFD adherence interventions. Methods Topical review of literature published since 2008 investigating GFD adherence in pediatric samples. Results Reviews of pediatric studies indicate GFD nonadherence rates ranging from 19 to 56%. There are few evidence-based, published pediatric GFD adherence interventions. Novel assessments of GFD adherence are promising but require further study. Nonmodifiable and modifiable factors within individual, family, community, and health systems domains must be considered when developing future interventions. Clinical implications are discussed. Conclusions Avenues for future research include development and refinement of adherence assessment tools and development of evidence-based GFD adherence interventions. Novel technologies (e.g., GFD mobile applications) require empirical study but present exciting opportunities for adherence intervention.
Antenatal corticosteroid treatment: factors other than lung maturation

Abstract Antenatal corticosteroid (CS) therapy improves both fetal lung mechanism and gas exchange due to accelerated morphologic development of type one and two pneumocytes. This therapy also enhances the production of surfactant binding proteins and fetal lung antioxidant enzymes. In women with threatening preterm delivery, a single course is advocated between 24 and 34 weeks’ gestation with either betamethasone (two doses of 12 mg 24 h apart) or dexamethasone (four doses of 6 mg at 12-h intervals). Such treatment reduces the rate of respiratory distress syndrome, comorbidity, and mortality in neonates in the first 48 h of life. The optimal time interval between CS administration and delivery is reported to be 1–7 days. Weekly repeat courses reduce the occurrences and severity of respiratory diseases but are associated with reduce fetal growth. Multiple courses should be avoided. However, a repeat course should be considered in women at risk of preterm birth 7 or more days after an initial course in women who remain at risk of preterm birth <34 weeks’ gestation. CS may be harmful in growth restricted fetuses associated with an absent or reversed end-diastolic UA flow since they are at increased risk of acidosis and perinatal death. The purpose of this publication is to update and highlight antenatal CS therapy.
Distributed Optimal Reactive Power Control of Power Systems

To accommodate the increasing penetration level of distributed generators (DGs) in the electrical energy power system, appropriate reactive power control of DGs, which can lead to the voltage profile improvement and power loss minimization, should be addressed. This paper proposed a consensus-based distributed algorithm for the reactive power control of DGs in the power system to optimize the multi-objective function, which includes power loss, voltage deviation, and cost of the reactive power generation of DGs. The formulated problem is proved to be convex. The proposed algorithm is tested on 6- and 34-bus systems to validate its effectiveness and scalability. The proposed algorithm is also compared with the centralized technique particle swarm optimization (PSO), which demonstrates the effectiveness of the proposed distributed algorithm.
Wavelet-Based Image Deconvolution and Reconstruction

Image deconvolution and reconstruction are inverse problems which are encountered in a wide array of applications. Due to the ill-posedness of such problems, their resolution generally relies on the incorporation of prior information through regularizations, which may be formulated in the original data space or through a suitable linear representation. In this article, we show the benefits which can be drawn from frame representations, such as wavelet transforms. We present an overview of recovery methods based on these representations: (i) variational formulations and non-smooth convex optimization strategies, (ii) Bayesian approaches, especially Monte Carlo Markov Chain methods and variational Bayesian approximation techniques, and (iii) Stein-based approaches. A brief introduction to blind deconvolution is also provided.
t-Darpp Activates IGF-1R Signaling to Regulate Glucose Metabolism in Trastuzumab-Resistant Breast Cancer Cells

Purpose: Increased glycolysis and glucose dependence is a hallmark of malignancy that enables tumors to maximize cell proliferation. In HER2+ cancers, an increase in glycolytic capacity is associated with trastuzumab resistance. IGF-1R activation and t-Darpp overexpression both confer trastuzumab resistance in breast cancer. We therefore investigated a role for IGF-1R and t-Darpp in regulating glycolytic capacity in HER2+ breast cancers. Experimental Design: We examined the relationship between t-Darpp and IGF-1R expression in breast tumors and their respective relationships with patient survival. To assess t-Darpp's metabolic effects, we used the Seahorse flux analyzer to measure glucose metabolism in trastuzumab-resistant SK-BR-3 cells (SK.HerR) that have high endogenous t-Darpp levels and SK.tDrp cells that stably overexpress exogenous t-Darpp. To investigate t-Darpp's mechanism of action, we evaluated t-Darpp:IGF-1R complexes by coimmunoprecipitation and proximity ligation assays. We used pathway-specific inhibitors to study the dependence of t-Darpp effects on IGF-1R signaling. We used siRNA knockdown to determine whether glucose reliance in SK.HerR cells was mediated by t-Darpp. Results: In breast tumors, PPP1R1B mRNA levels were inversely correlated with IGF-1R mRNA levels and directly associated with shorter overall survival. t-Darpp overexpression was sufficient to increase glucose metabolism in SK.tDrp cells and essential for the glycolytic phenotype of SK.HerR cells. Recombinant t-Darpp stimulated glucose uptake, glycolysis, and IGF-1R–Akt signaling in SK-BR-3 cells. Finally, t-Darpp stimulated IGF-1R heterodimerization with ErbB receptors and required IGF-1R signaling to confer its metabolic effects. Conclusions: t-Darpp activates IGF-1R signaling through heterodimerization with EGFR and HER2 to stimulate glycolysis and confer trastuzumab resistance. Clin Cancer Res; 24(5); 1216–26. ©2017 AACR.
Detecting Events in Evolving Social Networks through Node Centrality Analysis

Social networks have an evolving characteristic because of continuous interaction between users. Existing event detection tasks do not consider the analysis under a user-centric perspective. In this paper we propose to detect node centrality events, that is the task of ﬁnding events based on the position and roles of the nodes. We present a naive algorithm for detecting such events in network streams. Moreover, we apply our proposal in a case study, showing how node centrality events can be used for tracking user preferences changes.
A Negative Regulator in Response to Salinity in Rice: Oryza sativa Salt-, ABA- and Drought-Induced RING Finger Protein 1 (OsSADR1)

RING (Really Interesting New Gene) finger proteins play crucial roles in abiotic stress responses in plants. We report the RING finger E3 ligase gene, an Oryza sativa salt, ABA and drought stress-induced RING finger protein 1 gene (OsSADR1). We demonstrated that although OsSAR1 possesses E3 ligase activity, a single amino acid substitution (OsSADR1C168A) in the RING domain resulted in no E3 ligase activity, suggesting that the activity of most E3s is specified by the RING domain. Additional assays substantiated that OsSADR1 interacts with three substrates-no E3 ligase acti and OsPIRIN, and mediates their proteolysis via the 26S proteasome pathway. For OsSADR1, approximately 62% of the transient signals were in the cytosol and 38% in the nucleus. However, transiently expressed OsSADR1 was primarily expressed in the nucleus (70%) in 200 mM salt-treated rice protoplasts. The two nucleus-localized proteins (OsSNAC2 and OsGRAS44) interacted with OsSADR1 in the cytosol and nucleus. Heterogeneous overexpression of OsSADR1 in Arabidopsis resulted in sensitive phenotypes for salt- and mannitol-responsive seed germination and seedling growth. With ABA, OsSADR1 overexpression in plants produced highly tolerant phenotypes, with morphological changes in root length and stomatal closure. The ABA-tolerant transgenic plants also showed hypersensitivity phenotypes under severe water deficit conditions. Taken together, OsSADR1 may act as a regulator in abiotic stress responses by modulating target protein levels.