Miracle-dz/UniFAR-FTUs huggingface dataset:
Whole-Exome Sequencing of Salivary Gland Mucoepidermoid Carcinoma

Purpose: Mucoepidermoid carcinoma (MEC) is the most common salivary gland malignancy. To explore the genetic origins of MEC, we performed systematic genomic analyses of these tumors. Experimental Design: Whole-exome sequencing and gene copy-number analyses were performed for 18 primary cancers with matched normal tissue. FISH was used to determine the presence or absence of the MECT1-MAML2 translocation in 17 tumors. Results: TP53 was the most commonly mutated gene in MEC (28%), and mutations were found only in intermediate- and high-grade tumors. Tumors with TP53 mutations had more mutations overall than tumors without TP53 mutations (P = 0.006). POU6F2 was the second most frequently mutated gene, found in three low-grade MECs with the same in-frame deletion. Somatic alterations in IRAK1, MAP3K9, ITGAL, ERBB4, OTOGL, KMT2C, and OBSCN were identified in at least two of the 18 tumors sequenced. FISH analysis confirmed the presence of the MECT1-MAML2 translocation in 15 of 17 tumors (88%). Conclusions: Through these integrated genomic analyses, MECT1-MAML2 translocation and somatic TP53 and POU6F2 mutations appear to be the main drivers of MEC. Clin Cancer Res; 23(1); 283–8. ©2016 AACR.
p53: the ultimate tumor suppressor gene?

Alterations in the gene encoding the cellular p53 protein are perhaps the most frequent type of genetic lesions in human cancer. At the heart of these alterations is the abrogation of the tumor suppressor activity of the normal p53. In many cases this is achieved through point mutations in p53, which often result in pronounced conformational changes. Such mutant polypeptides, which tend to accumulate to high levels in cancer cells, are believed to exert a dominant negative effect over coexpressed normal p53. Extensive research on p53, especially in the course of the last 3 years, has already provided much insight into the biological and biochemical mechanisms that underlie its capacity to act as a potent tumor suppressor. There are now many indications that p53 may play a central role in the control of cell proliferation, cell survival, and differentiation. Nevertheless, despite the purported importance of p53 for such crucial processes, mice can develop apparently without any defect in the total absence of p53. This raises the possibility that p53 may become critically limiting only when normal growth control is lost. — Oren, M. p53: the ultimate tumor suppressor gene? FASEB J. 6: 3169‐3176; 1992.
Event-triggered H∞ control for switched linear systems with time delay

This paper studies the event-triggered H∞ control of switched linear systems with time delay. In the framework of state feedback control, an event-triggering strategy is adopted to replace the traditional periodic sampling strategy. By utilizing such strategy, the state is sampled and transmitted if and only if the defined event-triggering condition is satisfied. Specifically, first, sufficient analysis conditions for the stabilization of switched closed-loop system with time delay are developed by using multiple Lyapunov functions approach and linear matrix inequalities (LMIs) technique. Consequently, sufficient design conditions for solving the event-triggered controllers' parameters are presented. Then, to avoid continuously sampling/triggering, Zeno behavior is discussed. Finally, numerical simulations verify the effectiveness of the proposed method.
A Test of the Modigliani-Miller Invariance Theorem and Arbitrage in Experimental Asset Markets

Modigliani and Miller show that the total market value of a firm is unaffected by a repackaging of asset return streams to equity and debt if pricing is arbitrage‐free. We investigate this invariance theorem in experimental asset markets, finding value‐invariance for assets of identical risks when returns are perfectly correlated. However, exploiting price discrepancies has risk when returns have the same expected value but are uncorrelated, in which case the law of one price is violated. Discrepancies shrink in consecutive markets, but persist even with experienced traders. In markets where overall trader acuity is high, assets trade closer to parity.
Clinical Management of Chronic Nightmares: Imagery Rehearsal Therapy

Problems with nightmares are reported by a sizable proportion of individuals with a history of trauma and by approximately 5% to 8% of the general population. Chronic nightmares may represent a primary sleep disorder rather than a symptom of a psychiatric disorder, and direct targeting of nightmares is a feasible clinical approach to the problem. Of the treatments proposed, imagery rehearsal therapy (IRT) has received the most empirical support. An up-to-date account of this cognitive-imagery approach shows how to treat nightmares during 4 roughly 2-hr sessions. The main points covered in each therapy session and their underlying rationale are presented. Dismantling protocols are suggested to discern active ingredients of IRT and to develop flexible applications based on patients' needs.
Prevalence study of proximal vertebral artery stenosis using high‐resolution contrast‐enhanced magnetic resonance angiography

Purpose: To evaluate the prevalence of proximal vertebral artery stenosis, compared with those of the distal vertebral/basilar artery and extracranial internal carotid artery, in a large population of stroke and non‐stroke patients. Material and Methods: Nine‐hundred‐and‐thirty‐five patients who underwent high‐resolution contrast‐enhanced magnetic resonance angiography in a regional general hospital were categorized into six groups based on neurological symptoms and disease: an asymptomatic group (n = 182), a minor symptom group with headache or dizziness (n = 519), a cardiac group with coronary artery steno‐occlusive disease (n = 15), a hemorrhagic group with old cerebral hemorrhage (n = 26), an anterior circulation infarct group (n = 121), and posterior circulation infarct group (n = 72). Prevalence of stenosis of the proximal vertebral artery, distal vertebral/basilar artery, and internal carotid artery was analyzed. Results: The prevalence of stenosis of the proximal vertebral artery, distal vertebral/basilar artery, and internal carotid artery was 12.9%, 5.5%, and 7.2%, respectively, in the study population, and rose as the age increased (P<0.0001 for all arteries). The prevalence of stenosis of the proximal vertebral artery, distal vertebral/basilar artery, and internal carotid artery was 3.3%, 0.5%, and 1.1%, respectively, in the asymptomatic group; 8.3%, 2.1%, and 3.7%, respectively, in the minor symptom group; 13.3%, 6.7%, and 6.7%, respectively, in the cardiac group; 19.2%, 7.7%, and 7.7%, respectively, in the hemorrhagic group; 27.3%, 8.3%, and 25.6%, respectively, in the anterior circulation infarct group; and 44.4%, 36.1%, and 16.7%, respectively, in the posterior circulation infarct group. This increasing tendency of stenosis accordingly was statistically significant (P<0.0001 for all arteries). Conclusion: The prevalence of proximal vertebral artery stenosis was highest, compared with those of the distal vertebral/basilar artery and internal carotid artery, although the clinical significance of proximal vertebral artery stenosis should be investigated in further studies.
Fact-Checking in the Digital Journalistic Ecosystem: practices, Possibilities and Legitimation

This article surveys how fact-checking platforms make themselves legitimate as trustworthy institutions in contemporary journalism. The objective is to understand their contributions and challenges in the digital ecosystem, in which new actors, technologies and informative demands arise. As academic references, we work with the studies of Graves and Cherubini (2013) and Stencel (2017) about fact-checking’s evolution and analyze the fact-checkers’ guiding principles listed by The International Fact-checking Network (2016). The analysis presented on this paper is focused on Brazilian fact-checking projects Aos Fatos, Lupa and Truco no Congresso. We observe their organization and work methods and examine how they classify checked information, relating them to the Charaudeau’s research (2013) about proof’s production and truth value. We argue that fact-checking has become more significant in the media’s global coverage of political and administrate events due to its efforts to provide readers relevant and reliable information.
Neurodegeneration and the Circadian Clock

Despite varied etiologies and symptoms, several neurodegenerative diseases—specifically, Alzheimer’s (AD), Parkinson’s (PD), and Huntington’s diseases (HDs)—share the common feature of abnormal circadian rhythms, such as those in behavior (e.g., disrupted sleep/wake cycles), physiological processes (e.g., diminished hormone release) and biochemical activities (e.g., antioxidant production). Circadian disturbances are among the earliest symptoms of these diseases, and the molecular mechanisms of the circadian system are suspected to play a pivotal, and possibly causal, role in their natural histories. Here, we review the common circadian abnormalities observed in ADs, PDs and HDs, and summarize the evidence that the molecular circadian clockwork directly influences the course of these disease states. On the basis of this research, we explore several circadian-oriented interventions proposed as treatments for these neurological disorders.
Reduced expression and activation of voltage‐gated sodium channels contributes to blunted baroreflex sensitivity in heart failure rats

Voltage‐gated sodium (Nav) channels are responsible for initiation and propagation of action potential in the neurons. To explore the mechanisms of chronic heart failure (CHF)‐induced baroreflex dysfunction, we measured the expression and current density of Nav channel subunits (Nav1.7, Nav1.8, and Nav1.9) in the aortic baroreceptor neurons and investigated the role of Nav channels in aortic baroreceptor neuron excitability and baroreflex sensitivity in sham and CHF rats. CHF was induced by left coronary artery ligation. The development of CHF (6–8 weeks after the coronary ligation) was confirmed by hemodynamic and morphological characteristics. Immunofluorescent data indicated that Nav1.7 was expressed in A‐type (myelinated) and C‐type (unmyelinated) nodose neurons, but Nav1.8 and Nav1.9 were expressed only in C‐type nodose neurons. Real‐time RT‐PCR and Western blot data showed that CHF reduced mRNA and protein expression levels of Nav channels in nodose neurons. In addition, using the whole‐cell patch‐clamp technique, we found that Nav current density and cell excitability of the aortic baroreceptor neurons were lower in CHF rats than that in sham rats. Aortic baroreflex sensitivity was blunted in anesthetized CHF rats, compared with that in sham rats. Furthermore, Nav channel activator (rATX II, 100 nM) significantly enhanced Nav current density and cell excitability of aortic baroreceptor neurons and improved aortic baroreflex sensitivity in CHF rats. These results suggest that reduced expression and activation of the Nav channels are involved in the attenuation of baroreceptor neuron excitability, which subsequently contributes to the impairment of baroreflex in CHF state. © 2010 Wiley‐Liss, Inc.
Effect of initial fluid resuscitation on subsequent treatment in uncontrolled hemorrhagic shock in rats.

SUMMARY Using a modified uncontrolled hemorrhage shock model with massive splenic and vascular injury, we evaluated outcome and tissue oxidation injury with different resuscitation interventions during prehospital and hospital phases. The aim of our study was to explore the effect of initial fluid resuscitation on subsequent treatment of uncontrolled hemorrhagic shock in rats. Uncontrolled hemorrhagic shock was produced in 114 Wistar rat by sharp transection both of the splenic parenchyma at one location between the major branches of the splenic artery into the spleen and of one of the major branches of the splenic artery. Experimental design consisted of three phases: a "prehospital phase" (resuscitation with balanced saline to a mean arterial pressure (MAP) of 40, 50, 60, 80, and 100 mmHg, respectively, when MAP reached 30 mmHg), followed by a "hospital phase" (120 min, including control of hemorrhage and resuscitation with balanced saline and whole blood (2:1) or balanced saline alone to a MAP >80 mmHg), and a 240-min observation phase. Blood loss, infused volume, hematocrit, and survival rate were recorded. At the end of the experiment, survivors were sacrificed, and the lung, kidney, and distal ileum were harvested for determination of malondialdehyde (MDA) content and total antioxidative capacity (T-AOC). All rats that were resuscitated to a MAP >80 mmHg in the prehospital phase and received balanced saline alone in the hospital phase died, whereas those that had been resuscitated to a MAP of 40 or 50 mmHg during the prehospital phase and then resuscitated with balanced saline and whole blood in the hospital phase survived throughout the experiment. The animals whose MAP was kept higher than 80 mmHg had significantly higher MDA content and lower T-AOC than those whose MAP was maintained 40, 50, or 60 mmHg during the prehospital phase. In the hospital phase, resuscitation with balanced saline and whole blood not only relieved tissue damage but also improved the survival, as indicated by 44.4% survival rate in the rats that resuscitated to a MAP of 80 or 100 mmHg in the prehospital phase. These results suggested that in our uncontrolled hemorrhagic shock model, limited resuscitation in the prehospital phase had benefit for subsequent treatment in the hospital phase in terms of alleviated tissue damage and improved survivorship.
DNA polymerase from temperate phage Bam35 is endowed with processive polymerization and abasic sites translesion synthesis capacity

Significance Functional classification of DNA polymerases (DNAPs) usually divides them into replicative faithful replicases and error-prone enzymes devoted to DNA repair and DNA damage tolerance through translesion synthesis (TLS). When we analyzed the biochemical properties of phage Bam35 replicative DNAP, we found it to be a highly faithful DNAP that can couple strand displacement to processive DNA synthesis, suitable for rolling circle amplification of plasmidic DNA. Interestingly, it is also endowed with intrinsic TLS capacity opposite abasic sites and processive primer extension beyond the lesion. These features configure a versatile enzyme for accurate maintenance of viral genomic information over generations and, besides, to deal with DNA lesions, which suggest a possible application of Bam35 DNAP for the amplification of damaged or ancient DNA. DNA polymerases (DNAPs) responsible for genome replication are highly faithful enzymes that nonetheless cannot deal with damaged DNA. In contrast, translesion synthesis (TLS) DNAPs are suitable for replicating modified template bases, although resulting in very low-fidelity products. Here we report the biochemical characterization of the temperate bacteriophage Bam35 DNA polymerase (B35DNAP), which belongs to the protein-primed subgroup of family B DNAPs, along with phage Φ29 and other viral and mobile element polymerases. B35DNAP is a highly faithful DNAP that can couple strand displacement to processive DNA synthesis. These properties allow it to perform multiple displacement amplification of plasmid DNA with a very low error rate. Despite its fidelity and proofreading activity, B35DNAP was able to successfully perform abasic site TLS without template realignment and inserting preferably an A opposite the abasic site (A rule). Moreover, deletion of the TPR2 subdomain, required for processivity, impaired primer extension beyond the abasic site. Taken together, these findings suggest that B35DNAP may perform faithful and processive genome replication in vivo and, when required, TLS of abasic sites.
Radiation‐induced cerebral vasculopathy in children with neurofibromatosis and optic pathway glioma

Occlusive vasculopathy is a potential complication of radiotherapy in children with optic pathway glioma. With a median follow‐up of 7 years, 13 of 69 children in this study developed clinical and radiological signs of occlusive vasculopathy after radiotherapy within a median interval of 36 months. The major risk factor was neurofibromatosis type 1. Radiotherapy should no longer be the first treatment in these settings. When radiotherapy is unavoidable, regular screening for cerebral vasculopathy is mandatory, as preventive treatment is available. Ann Neurol 1999;45:393–396
Structure-based analysis of dynamic engineering process behavior

The dynamic behavior of complex systems is a well-known challenge within engineering. The major drawback of dependency modeling approaches for system analysis such as the Design Structure Matrix is that they depict a static view on the system and therefore only allow very limited statements about the dynamic behavior of systems even though the structure mainly defines the system's behavior. Approaches to model the dynamic behavior of complex systems such as System Dynamics, do not offer the possibilities of dependency modeling, as static aspects such as the underlying structure of the system cannot be easily described. This paper proposes a framework for a structure-based analysis of the dynamic behavior of systems and combines dependency modeling approaches and System Dynamics. The framework can be used as an approach to generate dynamic system understanding, decision support through simulation experiments and benchmark different process structures by analyzing the relationship between underlying structure and dynamic behavior of the system. This allows for a projection of the performance of the system over time, based on its structure. The paper gives an overview of the framework, including the initial structural Multiple Domain Matrix model, the dynamizing and customizing of the model, model verification, the simulation of different variants of the underlying system structure and the analysis of the system structure based on the simulation results. The framework is applied within an exemplary case study where two different system structures of a design process are analyzed.
Ternary complex formation between AmtB, GlnZ and the nitrogenase regulatory enzyme DraG reveals a novel facet of nitrogen regulation in bacteria

Ammonium movement across biological membranes is facilitated by a class of ubiquitous channel proteins from the Amt/Rh family. Amt proteins have also been implicated in cellular responses to ammonium availability in many organisms. Ammonium sensing by Amt in bacteria is mediated by complex formation with cytosolic proteins of the PII family. In this study we have characterized in vitro complex formation between the AmtB and PII proteins (GlnB and GlnZ) from the diazotrophic plant‐associative bacterium Azospirillum brasilense. AmtB–PII complex formation only occurred in the presence of adenine nucleotides and was sensitive to 2‐oxoglutarate when Mg2+ and ATP were present, but not when ATP was substituted by ADP. We have also shown in vitro complex formation between GlnZ and the nitrogenase regulatory enzyme DraG, which was stimulated by ADP. The stoichiometry of this complex was 1:1 (DraG monomer : GlnZ trimer). We have previously reported that in vivo high levels of extracellular ammonium cause DraG to be sequestered to the cell membrane in an AmtB and GlnZ‐dependent manner. We now report the reconstitution of a ternary complex involving AmtB, GlnZ and DraG in vitro. Sequestration of a regulatory protein by the membrane‐bound AmtB–PII complex defines a new regulatory role for Amt proteins in Prokaryotes.
Exploring the English language teachers’ perceptions of plagiarism: The case of Algerian Universities

Academic dishonesty is an alarming issue in higher education which spreads increasingly into the academic discourse community. As such, the present study is concerned with the exploration of university English language teachers’ perceptions towards what might most bring about plagiarism among their students. The study attempted to figure out, through the teachers’ academic experiences regarding plagiarism, the main reasons behind students’ inclination to approach this issue at Algerian Universities. This piece of research helps to awake both the teachers and students’ vigilance in response to plagiarism as one of the most alarming acts of academic dishonesty, and, consequently, to diminish this academic corruption. To achieve the aim of the study, the researcher used an English language teachers' questionnaire adapted from a study conducted by Rezanejad & Rezaei (2013). A sample of eighty university English language teachers from Saida University and other Algerian universities were selected to respond to the questionnaire. However, only 36 copies of the questionnaire were filled out and returned. The results of the present research indicated that Algerian university English teachers believe that their students had different reasons for plagiarism but they mostly plagiarize because of their bad command of the language and easiness of plagiarism.
Household gas cooking: a risk factor for respiratory illnesses in preschool children

Aims: To explore the association of household gas cooking and respiratory illnesses in preschool children and their relation to outdoor air pollution. Methods: Cross-sectional study among households that used gas stoves for cooking in two housing estates with contrasting air qualities in Hong Kong. A structured questionnaire was administered to parents of 426 children aged 0–6 years on their exposure to gas cooking and passive smoking, and the prevalence of respiratory illnesses. Results: A total of 111 children (26.1%) were reported to have one or more respiratory illnesses (allergic rhinitis, asthma, bronchitis, sinusitis, and pneumonia). Of these, 21 (18.9%), 41 (36.9%), and 49 (44.1%) children were from households that cooked once, twice, and three times a day with gas. Hierarchical logistic regression models adjusting for socioeconomic, demographic, and indoor risk factors including passive smoking showed that household gas cooking was positively associated with respiratory illnesses. There was a dose-response relation between the frequency of gas cooking and the prevalence of respiratory illnesses in the estate with lower outdoor air pollution (OR = 6.1 and 3.2 respectively, for cooking three and two meals a day, compared to one meal a day). This relation was not observed in the more polluted estate. The association between the presence of a cigarette smoker in the household and the prevalence of respiratory illnesses was not significant. Conclusions: As gas cooking is common in urban households, the findings could have important public health implications.