Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of plasma exchange on in-hospital mortality in patients with pulmonary hemorrhage secondary to antineutrophil cytoplasmic antibody-associated vasculitis: A propensity-matched analysis using a nationwide administrative database

Background Secondary pulmonary hemorrhage increases the risk of mortality in patients with antineutrophil cytoplasmic antibody-associated vasculitis (AAV); plasma exchange therapy may improve outcomes in these patients. We conducted a retrospective cohort study to investigate the effect of plasma exchange therapy on short-term prognoses in patients with pulmonary hemorrhage secondary to AAV. Methods This study utilized the Diagnosis Procedure Combination database, which is a nationwide inpatient database in Japan. We checked the abstract data and medical actions and identified the patients with pulmonary hemorrhage secondary to AAV who required proactive treatment between 2009 and 2014. To compare the in-hospital mortality, we performed propensity score matching between the plasma exchange and non-plasma exchange groups at a ratio of 1:1. Results Of the 52,932 patients with AAV, 940 developed pulmonary hemorrhage as a complication. A total of 249 patients from 194 hospitals were eligible for the study. Propensity score matching at a ratio of 1:1 was performed, and 59 pairs were formed (plasma exchange group, n = 59; non-plasma exchange group, n = 59). A statistically significant difference was found in the all-cause in-hospital mortality between the plasma exchange and non-plasma exchange groups (35.6% vs. 54.2%; p = 0041; risk difference, −18.6; 95% confidence interval (CI), −35.4% to −0.67%). Conclusion Thus, plasma exchange therapy was associated with improved in-hospital mortality in patients with pulmonary hemorrhage secondary to AAV.
Can NetGAN be improved by short random walks originated from dense vertices?

Graphs are useful structures that can model several important real-world problems. Recently, learning graphs have drawn considerable attention, leading to the proposal of new methods for learning these data structures. One of these studies produced NetGAN, a new approach for generating graphs via random walks. Although NetGAN has shown promising results in terms of accuracy in the tasks of generating graphs and link prediction, the choice of vertices from which it starts random walks can lead to inconsistent and highly variable results, especially when the length of walks is short. As an alternative to random starting, this study aims to establish a new method for initializing random walks from a set of dense vertices. We purpose estimating the importance of a node based on the inverse of its influence over the whole vertices of its neighborhood through random walks of different sizes. The proposed method manages to achieve significantly better accuracy, less variance and lesser outliers.
Towards Better Entity Linking Evaluation

The Entity Linking (EL) task is concerned with linking entity mentions in a text collection with their corresponding knowledge-base entries. Despite the progress made in the evaluation of EL systems, there is still much work to be done, where this Ph.D. research tackles issues concerning EL evaluation. Among these issues, we stress (a) the lack of consensus about the definition of “entity” and the lack of evaluation metrics that allow for different notions of entities, (b) the lack of datasets that allow for cross-language comparison, and (c) the focus on evaluating high-level systems rather than low-level techniques. By addressing these challenges and better understanding the performance of EL systems, our hypothesis is that we can create a more general, more configurable EL framework that can be better adapted to the needs of a particular application. In the early stages of this PhD work, we have identified these problems and begun to address (a) and (b), publishing initial results that constitute a significant step forward in our investigation. However, there are still further challenges that must be addressed before we reach our goal. Our next steps thus involve proposing a more fluid definition of “entity” adaptable to different applications, the definition of quality measures that allow for comparing EL approaches targeting different types of entities, as well as the creation of a customizable EL framework that allows for composing and evaluating individual techniques as appropriate to a particular task.
Rational Design of Packaging: Toward Safer and Ecodesigned Food Packaging Systems

It is necessary and urgent to reduce the impact of single-use plastics and in particular those used for beverages and similar products. Fewer plastics or reduced shelf-life need to be explored simultaneously while keeping open the possibilities of bringing on the innovative market designs and consumer experiences. This work details a general computational framework bridging simulation of coupled mass transfer and non-linear thermodynamics with 3D geometry optimization, ecodesign and other mass transfer-related risks (collapse, migration of chemicals). The three-dimensions (impacts, design, shelf-life) of the storage of alcoholic beverages in plastic containers are presented as a representative case-study of the multi-objective ecodesign problem and as an illustration of new trends to accelerate prototyping and innovation. The capacity to evaluate, maximize product shelf-life and minimize packaging waste was tested on 450 miniatures served usually in plane and train. Four alcoholic strengths (including pure water) and four storage conditions were considered. Several alternatives (900 different 3D designs) were explored by simulation and constrained optimization to reach the targeted shelf-life. The large set was used to establish the Pareto optimal design enabling to minimize weights while maximizing shelf-life. The approach is sufficiently versatile and flexible to adapt arbitrary designs and additional phenomena controlling shelf-life (aroma scalping, oxidation, migration of non-intentionally added substances).
Accuracy of Impedance Cardiography for Hemodynamic Assessment During Rest and Exercise in Wheelchair Rugby Players

ABSTRACT Purpose: The aim of the study was to analyze the accuracy of impedance cardiography (ICG) for hemodynamic assessment in wheelchair rugby players during rest and exercise. Method: The study included 21 players (mean age 33.0 ± 5.4, 86% male) with posttraumatic tetraplegia. ECG, echocardiography, and gas exchange analysis during rest and exercise were used to obtain heart rate (HR), stroke volume (SV), and cardiac output (CO) for comparison with PhysioFlow®. Results: There was a good correlation between reference methods and ICG for HR, SV, CO at rest and CO at peak exercise (r = 0.69–0.77, p < .001) and a very good correlation for peak HR (r = 0.91, p < .0001). ICG overestimated SV at rest, CO at rest, and peak CO, which resulted in low intraclass correlation coefficients (ICC = 0.250 and 0.570). Conclusions: ICG can serve as a good estimate of basic hemodynamic parameters during rest and exercise in wheelchair rugby players but overestimates stroke volume and cardiac output.
Residual Stress Extraction of Surface-Micromachined Fixed-Fixed Nickel Beams Using a Wafer-Scale Technique

This paper reports on the extraction of residual stress in surface-micromachined nickel thin films of electrostatically actuated fixed-fixed beams using a wafer-scale technique. The distribution of residual stress for 87 beams on a 4-in quarter wafer piece is presented. The residual stress (σ0) is determined from the best fit of the displacement-voltage curves predicted by a computationally efficient model to the experimental data. The nondestructive and automated measurements are taken at room temperature and directly at the beam itself without any additional test structures. The model employed incorporates the nonideal effects of inclined supports, nonflat initial beam profiles, and fringing fields. The extracted residual stress values vary between -12.8 and 13.6 MPa (negative values are for compressive stresses and positive ones for tensile stresses). The residual stresses for these 87 beams follow a nearly normal distribution with a mean value of -1.7 MPa and a standard deviation of 5.9 MPa, which represents the variability of the residual stresses across the wafer. Detailed uncertainty analysis has been conducted, and it reveals that inaccurate modeling of the nonideal effects will result in significant errors in the extracted residual stress. Although demonstrated on nickel thin films, this technique can be applied to other metallic thin films.
Selective Inhibition of the Expression of Signal Transduction Proteins by Lithium in Nerve Growth Factor‐Differentiated PC12 Cells

Abstract: This investigation examined if lithium, the primary therapeutic treatment for bipolar affective disorder, modulated the levels of selected signal transduction proteins in PC12 cells. Nerve growth factor (NGF) induced differentiation of PC12 cells, and after 12 days of NGF treatment there were large increases in the levels of the heterotrimeric G protein subunits αo1, αi1, β, and αs, small increases in those of αi2 and αq, and a slight decrease in that of αo2. Lithium (1 mM, equivalent to the therapeutic concentration) selectively reduced NGF‐induced increases in levels of G protein subunits, generally having the greatest inhibition on those that were increased the most by NGF. Lithium at 5 mM had greater inhibitory effects than 1 mM lithium on NGF‐induced increases in levels of G proteins, but neither concentration of lithium affected the induction of the cytoskeletal protein β‐tubulin. Examination of other proteins involved in signal transduction revealed that 12 days of NGF treatment increased the level of protein kinase C‐α, but not those of the β, ε, or ζ subtypes, and did not alter the levels of β, γ, or δ phospholipase C. Pretreatment with lithium inhibited the increase in content of protein kinase C‐α induced by NGF but had little effect on the proteins not responsive to NGF except for decreasing the levels of protein kinase C‐ε. The inhibitory effect of lithium was found not to be due to inhibition of NGF‐induced tyrosine phosphorylation, which was unaffected by 5 mM lithium, or to inositol depletion. In summary, use of the dynamic system of NGF‐induced PC12 cell differentiation provided a sensitive model in which to identify signal transduction proteins that were influenced by lithium treatment. The large changes caused by a therapeutically equivalent concentration of lithium lend support to the proposal that the selective inhibitory effects of lithium on subtypes of G proteins and protein kinase C may be important therapeutic targets.
Use of biologics in chronic sinusitis with nasal polyps.

PURPOSE OF REVIEW Chronic rhinosinusitis with nasal polyps (CRSwNP) is a heterogeneous inflammatory condition with different endotypes between patients from eastern or western countries. Targeted biologics are currently used to treat CRSwNP, but the outcomes widely vary. This review focuses on the present use of biologics for treating CRSwNP. RECENT FINDINGS Monoclonal biologics have been used as an innovative therapy for multiple allergic diseases and comorbid allergic conditions. Over the past several decades, numerous biomarkers have been investigated and were found to be closely correlated with CRSwNP, improving the understanding of inflammatory patterns and endotype classifications for CRSwNP and prompting discussion regarding the use of biologics in CRSwNP. Efficacies vary in reports of different research groups, but it has been found that patients with TH-2-driven inflammatory patterns respond better to the use of biologics than those with non-TH-2-driven CRSwNP. These findings suggest the importance and urgency of developing criteria for biologics in CRSwNP. SUMMARY Precisely determining patient criteria, identifying treatment biomarkers based on endotyping for CRSwNP and determinations of contraindications for long-term utilization may be useful for optimizing treatment strategies and improving the therapeutic efficacy of biologics to achieve long-term control starting at early stages.
Measurement of cytotoxic activity in experimental cancer

Several tumor cell systems have been developed for investigating the cytotoxic activity of different substances. The Ehrlich ascytic tumor (EAT) has been studied extensively and used to increase our comprehension of immunotherapy (Yamamoto and Naraparaju. Cancer Res 57:2187–2192, 1997). In this study, we evaluated the ability of an enzymatic method to assess cytotoxic tumor activity in vitro. To prepare cytotoxic cells, lymphoid cells isolated from the lymph nodes of C57BL/6 mice were activated with interleukin‐2 (IL‐2). The cytotoxic activity to EAT cells was assessed by an enzymatic test using lactate dehydrogenase (LDH), an enzyme widely distributed in mammalian tissues which, in the presence of NAD/NADH, converts lactate to pyruvate. IL‐2 treatment of lymph node cells induced a greater percentage of lysis (75.47%) than effector cells that were not treated with IL‐2 (42.38%). This suggests that IL‐2 directly activates effector cells and not tumor cells. The results demonstrate that the LDH release‐measurement method can be utilized to assay cytotoxic cell‐mediated activity in which murine tumor cells act as the target. Levels of IL‐2 appear to have a direct correlation to cellular immunity and treatment with these substances may strengthen immune function and decrease the pace of disease development. J. Clin. Lab. Anal. 18:27–30, 2004. © 2004 Wiley‐Liss, Inc.
I Am Conscious, Therefore, I Am: Imagery, Affect, Action, and a General Theory of Behavior

Organisms are adapted to each other and the environment because there is an inbuilt striving toward security, stability, and equilibrium. A General Theory of Behavior connects imagery, affect, and action with the central executive system we call consciousness, a direct emergent property of cerebral activity. The General Theory is founded on the assumption that the primary motivation of all of consciousness and intentional behavior is psychological homeostasis. Psychological homeostasis is as important to the organization of mind and behavior as physiological homeostasis is to the organization of bodily systems. Consciousness processes quasi-perceptual images independently of the input to the retina and sensorium. Consciousness is the “I am” control center for integration and regulation of (my) thoughts, (my) feelings, and (my) actions with (my) conscious mental imagery as foundation stones. The fundamental, universal conscious desire for psychological homeostasis benefits from the degree of vividness of inner imagery. Imagery vividness, a combination of clarity and liveliness, is beneficial to imagining, remembering, thinking, predicting, planning, and acting. Assessment of vividness using introspective report is validated by objective means such as functional magnetic resonance imaging (fMRI). A significant body of work shows that vividness of visual imagery is determined by the similarity of neural responses in imagery to those occurring in perception of actual objects and performance of activities. I am conscious; therefore, I am.
Cross-Reactivity as a Mechanism Linking Infections to Stroke

The relevance of infections as risk factor for cerebrovascular disease is being increasingly recognized. Nonetheless, the pathogenic link between the two entities remains poorly understood. Consistent with recent advances in medicine, the present work addresses the hypothesis that infection-induced immune responses may affect human proteins associated with stroke. Applying established procedures in bioinformatics, the pathogen antigens and the human proteins were searched for common sequences using pentapeptides as probes. The resulting data demonstrate massive peptide sharing between infectious pathogens—such as Chlamydia pneumoniae, Streptococcus pneumoniae, Tannerella forsythia, Haemophilus influenzae, Influenza A virus, and Cytomegalovirus—and human proteins related to risk of ischemic and hemorrhagic stroke. Moreover, the shared peptides are also evident in a number of epitopes experimentally proven immunopositive in the human host. The present findings suggest cross-reactivity as a potential mechanistic link between infections and stroke.
Direct retrieval method of the effective permittivity and permeability of bulk semi-infinite metamaterials by variable-angle spectroscopic ellipsometry

In this work, we present a simple method for the direct retrieval of the effective permittivity and permeability of a bulk semi-infinite metamaterial from variable-angle spectroscopic ellipsometry measurements. Starting from the well-known Fresnel equations, we derive an analytical expression in which unknown coefficients are fitted to the experimental data using a linear regression model. The effective permittivity and permeability are then determined by solving a simple system and the correct solution is selected based on physical criteria. As an example, the method is applied to the case of a self-assembled metamaterial exhibiting strong isotropic optical magnetism.
Further improving of upper bound on a geometric Ramsey problem

We consider following geometric Ramsey problem: find the least dimension $n$ such that for any 2-coloring of edges of complete graph on the points $\{\pm 1\}^n$ there exists 4-vertex coplanar monochromatic clique. Problem was first analyzed by Graham and Rothschild and they gave an upper bound: $n\le F(F(F(F(F(F(F(12)))))))$, where $F(m) = 2\uparrow^m3$. In 2014 Lavrov, Lee and Mackey greatly improved this result by giving upper bound $n< 2\uparrow\uparrow\uparrow 6 < F(5)$. In this paper we revisit their estimates and reduce upper bound to $n< 2\uparrow\uparrow\uparrow 5$
The KAT5-Acetyl-Histone4-Brd4 axis silences HIV-1 transcription and promotes viral latency

The bromodomain protein Brd4 promotes HIV-1 latency by competitively inhibiting P-TEFb-mediated transcription induced by the virus-encoded Tat protein. Brd4 is recruited to the HIV LTR by interactions with acetyl-histones3 (AcH3) and AcH4. However, the precise modification pattern that it reads and the writer for generating this pattern are unknown. By examining a pool of latently infected proviruses with diverse integration sites, we found that the LTR characteristically has low AcH3 but high AcH4 content. This unusual acetylation profile attracts Brd4 to suppress the interaction of Tat with the host super elongation complex (SEC) that is essential for productive HIV transcription and latency reversal. KAT5 (lysine acetyltransferase 5), but not its paralogs KAT7 and KAT8, is found to promote HIV latency through acetylating H4 on the provirus. Antagonizing KAT5 removes AcH4 and Brd4 from the LTR, enhances the SEC loading, and reverses as well as delays, the establishment of latency. The pro-latency effect of KAT5 is confirmed in a primary CD4+ T cell latency model as well as cells from ART-treated patients. Our data thus indicate the KAT5-AcH4-Brd4 axis as a key regulator of latency and a potential therapeutic target to reactivate latent HIV reservoirs for eradication.
Intestinal Inflammation in Children with Cystic Fibrosis Is Associated with Crohn’s-Like Microbiota Disturbances

Cystic fibrosis (CF) is a systemic genetic disease that leads to pulmonary and digestive disorders. In the majority of CF patients, the intestine is the site of chronic inflammation and microbiota disturbances. The link between gut inflammation and microbiota dysbiosis is still poorly understood. The main objective of this study was to assess gut microbiota composition in CF children depending on their intestinal inflammation. We collected fecal samples from 20 children with CF. Fecal calprotectin levels were measured and fecal microbiota was analyzed by 16S rRNA sequencing. We observed intestinal inflammation was associated with microbiota disturbances characterized mainly by increased abundances of Staphylococcus, Streptococcus, and Veillonella dispar, along with decreased abundances of Bacteroides, Bifidobacterium adolescentis, and Faecalibacterium prausnitzii. Those changes exhibited similarities with that of Crohn’s disease (CD), as evidenced by the elevated CD Microbial-Dysbiosis index that we applied for the first time in CF. Furthermore, the significant over-representation of Streptococcus in children with intestinal inflammation appears to be specific to CF and raises the issue of gut–lung axis involvement. Taken together, our results provide new arguments to link gut microbiota and intestinal inflammation in CF and suggest the key role of the gut–lung axis in the CF evolution.
Hepatitis B Virus Molecular Epidemiology, Host-Virus Interaction, Coinfection, and Laboratory Diagnosis in the MENA Region: An Update

Hepatitis B virus (HBV) is an enveloped partial double-stranded DNA virus that can cause acute and chronic hepatitis. According to the World Health Organization (WHO) and the Centers for Disease Control and Prevention (CDC), 257 million people are living with HBV. Moreover, 20,900 acute hepatitis B cases were reported in 2016. Hepatitis B is highly prevalent in the African, Western Pacific, Eastern Mediterranean, South-East Asia, and European regions, respectively. Due to the high mutational rate of HBV and lack of reverse transcriptase proofreading activity, ten different genotypes with different geographical distributions have been identified. HBV pathogenesis and severity of infection depend on several host and viral factors, particularly, the genetic variability of both the host and virus. Although HBV infection is a global health concern, there is a lack of adequate studies and reports in the Middle East and North Africa (MENA) region. Here, we provide a review on HBV epidemiology, pathogenesis, host–pathogen interactions, coinfection with selected viruses, and laboratory diagnosis, focusing on studies conducted in the MENA region to determine the current situation of the HBV infection and outline the future study areas.
Adenosine 2A Receptor Activation Attenuates Ischemia Reperfusion Injury During Extracorporeal Cardiopulmonary Resuscitation.

OBJECTIVE We tested the hypothesis that systemic administration of an A2AR agonist will reduce multiorgan IRI in a porcine model of ECPR. SUMMARY BACKGROUND DATA Advances in ECPR have decreased mortality after cardiac arrest; however, subsequent IRI contributes to late multisystem organ failure. Attenuation of IRI has been reported with the use of an A2AR agonist. METHODS Adult swine underwent 20 minutes of circulatory arrest, induced by ventricular fibrillation, followed by 6 hours of reperfusion with ECPR. Animals were randomized to vehicle control, low-dose A2AR agonist, or high-dose A2AR agonist. A perfusion specialist using a goal-directed resuscitation protocol managed all the animals during the reperfusion period. Hourly blood, urine, and tissue samples were collected. Biochemical and microarray analyses were performed to identify differential inflammatory markers and gene expression between groups. RESULTS Both the treatment groups demonstrated significantly higher percent reduction from peak lactate after reperfusion compared with vehicle controls. Control animals required significantly more fluid, epinephrine, and higher final pump flow while having lower urine output than both the treatment groups. The treatment groups had lower urine NGAL, an early marker of kidney injury (P = 0.01), lower plasma aspartate aminotransferase, and reduced rate of troponin rise (P = 0.01). Pro-inflammatory cytokines were lower while anti-inflammatory cytokines were significantly higher in the treatment groups. CONCLUSIONS Using a novel and clinically relevant porcine model of circulatory arrest and ECPR, we demonstrated that a selective A2AR agonist significantly attenuated systemic IRI and warrants clinical investigation.