Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparing Pandemic to Seasonal Influenza Mortality: Moderate Impact Overall but High Mortality in Young Children

Background We assessed the severity of the 2009 influenza pandemic by comparing pandemic mortality to seasonal influenza mortality. However, reported pandemic deaths were laboratory-confirmed – and thus an underestimation – whereas seasonal influenza mortality is often more inclusively estimated. For a valid comparison, our study used the same statistical methodology and data types to estimate pandemic and seasonal influenza mortality. Methods and Findings We used data on all-cause mortality (1999–2010, 100% coverage, 16.5 million Dutch population) and influenza-like-illness (ILI) incidence (0.8% coverage). Data was aggregated by week and age category. Using generalized estimating equation regression models, we attributed mortality to influenza by associating mortality with ILI-incidence, while adjusting for annual shifts in association. We also adjusted for respiratory syncytial virus, hot/cold weather, other seasonal factors and autocorrelation. For the 2009 pandemic season, we estimated 612 (range 266–958) influenza-attributed deaths; for seasonal influenza 1,956 (range 0–3,990). 15,845 years-of-life-lost were estimated for the pandemic; for an average seasonal epidemic 17,908. For 0–4 yrs of age the number of influenza-attributed deaths during the pandemic were higher than in any seasonal epidemic; 77 deaths (range 61–93) compared to 16 deaths (range 0–45). The ≥75 yrs of age showed a far below average number of deaths. Using pneumonia/influenza and respiratory/cardiovascular instead of all-cause deaths consistently resulted in relatively low total pandemic mortality, combined with high impact in the youngest age category. Conclusion The pandemic had an overall moderate impact on mortality compared to 10 preceding seasonal epidemics, with higher mortality in young children and low mortality in the elderly. This resulted in a total number of pandemic deaths far below the average for seasonal influenza, and a total number of years-of-life-lost somewhat below average. Comparing pandemic and seasonal influenza mortality as in our study will help assessing the worldwide impact of the 2009 pandemic.
Distinct Hemodynamic Changes After Interventional Mitral Valve Edge‐to‐Edge Repair in Different Phenotypes of Heart Failure: An Integrated Hemodynamic Analysis

Background Percutaneous mitral valve edge‐to‐edge repair (pMVR) with a MitraClip is beneficial for the clinical symptoms of patients irrespective of the ejection fraction (EF). Nevertheless, the consequences on hemodynamics are poorly understood. Therefore, we used data from noninvasive pressure‐volume loops to investigate the left ventricular (LV) remodeling of patients after pMVR dependent on their baseline EF. Methods and Results In 130 patients with successful pMVR, the end‐diastolic pressure‐volume relationship (EDPVR) and end‐systolic pressure‐volume relationship were estimated noninvasively from echocardiographic data. We compared EDPVR and end‐systolic pressure‐volume relationship at discharge and follow‐up between patients with a reduced EF (<40%) and patients with a mid‐ranged or preserved EF (≥40%). Reduced EF was present in 71 patients (54%). Mean follow‐up duration was 277±117 days. We observed a significant reduction in degree of mitral regurgitation and an improvement in functional status at follow‐up irrespective of baseline EF. In patients with a mid‐ranged or preserved EF, the EDPVR and end‐systolic pressure‐volume relationship were shifted leftwards, suggesting an improvement in LV function. In contrast, in patients with a reduced EF, EDPVR and end‐systolic pressure‐volume relationship remained stable, although comparison with the baseline data indicates a rightward shift of the EDPVR. This indicates that there is no improvement in LV function after pMVR in patients with reduced EF. Conclusions The pMVR is associated with improved clinical symptoms in all patient subgroups. However, it leads to different hemodynamic responses. In patients with mid‐ranged or preserved EF, we found reverse remodeling with reduced LV dilatation and increased contractility. In contrast, in patients with reduced EF, we observed no reverse remodeling and no improvement in LV function.
Etiologies of acute demyelinating optic neuritis: an observational study of 110 patients

New criteria for the diagnosis of multiple sclerosis (MS) and discovery of myelin oligodendrocyte glycoprotein (MOG) or aquaporin‐4 (AQP4) antibodies (Abs) have changed the management of optic neuritis (ON). Our aim was to specify, in view of these recent advances, the etiologies of acute demyelinating ON for consecutive patients.
HFL-RC System at SemEval-2018 Task 11: Hybrid Multi-Aspects Model for Commonsense Reading Comprehension

This paper describes the system which got the state-of-the-art results at SemEval-2018 Task 11: Machine Comprehension using Commonsense Knowledge. In this paper, we present a neural network called Hybrid Multi-Aspects (HMA) model, which mimic the human's intuitions on dealing with the multiple-choice reading comprehension. In this model, we aim to produce the predictions in multiple aspects by calculating attention among the text, question and choices, and combine these results for final predictions. Experimental results show that our HMA model could give substantial improvements over the baseline system and got the first place on the final test set leaderboard with the accuracy of 84.13%.
Function and Safety of Lentivirus-Mediated Gene Transfer for CSF2RA-Deficiency.

Hereditary pulmonary alveolar proteinosis (hPAP) is a rare disorder of pulmonary surfactant accumulation and hypoxemic respiratory failure caused by mutations in CSF2RA (encoding the granulocyte/macrophage colony-stimulating factor [GM-CSF] receptor α-chain [CD116]), which results in reduced GM-CSF-dependent pulmonary surfactant clearance by alveolar macrophages. While no pharmacologic therapy currently exists for hPAP, it was recently demonstrated that endotracheal instillation of wild-type or gene-corrected mononuclear phagocytes (pulmonary macrophage transplantation [PMT]) results in a significant and durable therapeutic efficacy in a validated murine model of hPAP. To facilitate the translation of PMT therapy to human hPAP patients, a self-inactivating (SIN) lentiviral vector was generated expressing a codon-optimized human CSF2RA-cDNA driven from an EF1α short promoter (Lv.EFS.CSF2RAcoop), and a series of nonclinical efficacy and safety studies were performed in cultured macrophage cell lines and primary human cells. Studies in cytokine-dependent Ba/F3 cells demonstrated efficient transduction, vector-derived CD116 expression proportional to vector copy number, and GM-CSF-dependent cell survival and proliferation. Using a novel cell line constructed to express a normal GM-CSF receptor β subunit and a dysfunctional α subunit (due to a function-altering CSF2RAG196R mutation) that reflects the macrophage disease phenotype of hPAP patients, it was demonstrated that Lv.EFS. CSF2RAcoop transduction restored GM-CSF receptor function. Further, Lv.EFS. CSF2RAcoop transduction of healthy primary CD34+ cells did not adversely affect cell proliferation or affect the cell differentiation program. Results demonstrate Lv.EFS. CSF2RAcoop reconstituted GM-CSF receptor α expression, restoring GM-CSF signaling in hPAP macrophages, and had no adverse effects in the intended target cells, thus supporting testing of PMT therapy of hPAP in humans.
Mirroring the Social Aspects of Speech and Actions: The Role of the Insula

Action and speech may take different forms, being expressed, for example, gently or rudely. These aspects of social communication, named vitality forms, have been little studied in neuroscience. In the present functional magnetic resonance imaging study, we investigated the role of insula in processing action and speech vitality forms. In speech runs, participants were asked to listen or imaging themselves to pronounce action verbs gently or rudely. In action runs, they were asked to observe or imaging themselves to perform actions gently or rudely. The results showed that, relative to controls, there was an activation of the dorso-central insula in both tasks of speech and action runs. The insula sector specific for action vitality form was located slightly more dorsally than that of speech with a large overlap of their activations. The psycho-physiological interaction analysis showed that the insular sector involved in action vitality forms processing is connected with the left hemisphere areas controlling arm actions, whereas the sector involved in speech vitality forms processing is linked with right hemisphere areas related to speech prosody. We conclude that the central part of the insula is a key region for vitality forms processing regardless of the modality by which they are conveyed or expressed.
Pilot Study of Antimicrobial Resistance in Northern Bobwhites (Colinus virginianus)

SUMMARY Antimicrobial resistance (AMR) is an important issue for both wildlife conservation and public health. The purpose of this study was to screen for AMR in fecal bacteria isolated from northern bobwhite (Colinus virginianus), a species that is an ecologically and economically important natural resource in the southern United States. The antimicrobial susceptibility profiles of 45 Escherichia coli isolates, 20 Enterococcus faecalis isolates, and 10 Enterococcus faecium isolates were determined using the SensititerTM microbroth dilution minimum inhibitory concentration (MIC) plate, AVIAN1F. Overall, E. coli isolates had high MIC values for the following classes of antimicrobials: aminocoumarins, beta-lactams, lincosamides, macrolides, florfenicol, and sulfonamides. Enterococcus faecalis and E. faecium isolates had high MICs for aminocyclitols, aminoglycosides, beta-lactams, lincosamides, and sulfonamides. Enterococcus faecalis isolates also showed high MICs for aminocoumarins, while E. faecium isolates had high MICs for trimethoprim/sulfamethoxazole and tetracycline. Based on available veterinary interpretive criteria, 15% and 33% of E. coli isolates were resistant to sulphathiazole and sulphadimethoxine, respectively. Intermediate susceptibility to florfenicol was seen with 17.8% of E. coli isolates. Twenty percent of E. faecalis and 80% of E. faecium isolates were resistant to high-concentration streptomycin. One third of E. faecalis and 70% of E. faecium isolates were intermediately susceptible to erythromycin. Ten percent of E. faecium isolates were resistant to tetracycline and oxytetracycline. A comparison of available MIC suggests that AMR in wild bobwhite is less severe than in domestic poultry. Further investigation is needed to determine the source of AMR in wild bobwhite.
Dental Biofilm and Laboratory Microbial Culture Models for Cariology Research

Dental caries form through a complex interaction over time among dental plaque, fermentable carbohydrate, and host factors (including teeth and saliva). As a key factor, dental plaque or biofilm substantially influence the characteristic of the carious lesions. Laboratory microbial culture models are often used because they provide a controllable and constant environment for cariology research. Moreover, they do not have ethical problems associated with clinical studies. The design of the microbial culture model varies from simple to sophisticated according to the purpose of the investigation. Each model is a compromise between the reality of the oral cavity and the simplification of the model. Researchers, however, can still obtain meaningful and useful results from the models they select. Laboratory microbial culture models can be categorized into a closed system and an open system. Models in the closed system have a finite supply of nutrients, and are also simple and cost-effective. Models in the open system enabled the supply of a fresh culture medium and the removal of metabolites and spent culture liquid simultaneously. They provide better regulation of the biofilm growth rate than the models in the closed system. This review paper gives an overview of the dental plaque biofilm and laboratory microbial culture models used for cariology research.
Crystal Structures of Human CaMKIα Reveal Insights into the Regulation Mechanism of CaMKI

Human calcium/calmodulin-dependent protein kinase I (CaMKI) plays pivotal roles in the nervous system. The activity of human CaMKI is regulated by a regulatory region including an autoinhibitory segment and a CaM-binding segment. We report here four structures of three CaMKIα truncates in apo form and in complexes with ATP. In an apo, autoinhibited structure, the activation segment adopts a unique helical conformation which together with the autoinhibitory segment constrains helices αC and αD in inactive conformations, sequesters Thr177 from being phosphorylated, and occludes the substrate-binding site. In an ATP-bound, inactive structure, the activation segment is largely disordered and the CaM-binding segment protrudes out ready for CaM binding. In an ATP-bound, active structure, the regulatory region is dissociated from the catalytic core and the catalytic site assumes an active conformation. Detailed structural analyses reveal the interplay of the regulatory region, the activation segment, and the nucleotide-binding site in the regulation of CaMKI.
It’s Only a Matter of Time

Intergenerational decisions affect other people in the future. The combination of intertemporal and interpersonal distance between decision makers in the present and other people in the future may lead one to expect little intergenerational generosity. In the experiments reported here, however, we posited that the negative effect of intertemporal distance on intergenerational beneficence would be reversed when people were primed with thoughts of death. This reversal would occur because death priming leads individuals to be concerned with having a lasting impact on other people in the future. Our experiments show that when individuals are exposed to death priming, the expected tendency to allocate fewer resources to others in the future, as compared with others in the present, is reversed. Our findings suggest that legacy motivations triggered by death priming can trump intergenerational discounting tendencies and promote intergenerational beneficence.
Employing Adaptive Finite Elements to Model Squeezing of a Layered Material in 3D

Finite element method (FEM) has long been an important tool for modeling a variety of processes including applications in mechanics [1], material science [2], [3], geology [4]-[6] and nanoengineering [7]. The hp-FEM is the most sophisticated version of the mesh adaptive algorithms [1], where elements are automatically h-refined (broken into smaller elements) or p-refined (polynomial order of approximating base is increased over selected elements). The decisions about finite elements that need to be refined are made iteratively based on the a posteriori error decrease estimate.
The Immunomodulatory Activity of Meningococcal Lipoprotein Ag473 Depends on the Conformation Made up of the Lipid and Protein Moieties

We have previously demonstrated that the meningococcal antigen Ag473 in the presence of Freund’s adjuvant can elicit protective immune responses in mouse challenge model. In this study, we evaluated the structural requirement for the immunological activity and the possible signaling pathway of recombinant Ag473 antigen produced in E. coli. We found that lipidated Ag473 (L-Ag473) possesses an intrinsic adjuvant activity that could be attributed to its ability to activate dendritic cells and promote their maturation. In addition, we found that L-Ag473 can activate human monocytes and promote maturation of human monocyte-derived dendritic cells. These results provide an indirect support that L-Ag473 may also be immunogenic in human. Interestingly, the observed activity is dependent on the overall conformation of L-Ag473 because heating and proteinase K treatment can diminish and abolish the activity. Furthermore, our data suggest a species-differential TLR recognition of L-Ag473. Overall, these data suggest a new paradigm for the ligand-TLR interaction in addition to demonstrating the self-adjuvanting activity of the vaccine candidate L-Ag473.
Loss of expression rather than cytoplasmic mislocalization of RUNX3 predicts worse outcome in non-small cell lung cancer

Functional inactivation of human runt-related transcription factor 3 (RUNX3) through mutation or epigenetic silencing has been well-documented in many cancerous entities. In addition to gene mutation and promoter hypermethylation, cytoplasmic mislocalization has emerged as another major manifestation of RUNX3 dysfunction in malignancies including breast, colorectal and gastric cancers. The aim of the present study was to investigate whether patients with non-small cell lung cancer (NSCLC) and different RUNX3 expression patterns would have different overall survival (OS), and the associations between different patterns of clinicopathological parameters and clinical outcome. Expressions of RUNX3 and Ki-67 were immunohistochemically detected in normal lung tissue (n=5) and surgically resected tissues from NSCLC patients (n=188). The optimal cutoff of RUNX3 was determined by X-tile software associated with their survival. Apoptotic index in cancerous tissue was evaluated using the terminal deoxynucleotidyl transferase mediated dUTP-biotin nick end labelling method. The prognostic significance of different expression patterns of RUNX3 was determined by means of Kaplan-Meier survival estimates and log-rank tests. It was revealed that loss of RUNX3 expression in NSCLC was correlated with a low cancerous apoptotic index (P<0.001), shorter OS and worse prognosis (P=0.0142), while no statistical difference of apoptotic index (P=0.73) or survival (P=0.3781) was determined between patient subgroups with different localization of RUNX3 expression, which was quite different from the situation demonstrated in other malignancies. In conclusion, loss of expression rather than cytoplasmic mislocalization of RUNX3 predicted worse outcome in NSCLC, which was quite different from what manifested in other cancer types, and thus, the underlying mechanism may deserve further investigation.
Reformulating Discourse Connectives for Non-Expert Readers

In this paper we report a behavioural experiment documenting that different lexico-syntactic formulations of the discourse relation of causation are deemed more or less acceptable by different categories of readers. We further report promising results for automatically selecting the formulation that is most appropriate for a given category of reader using supervised learning. This investigation is embedded within a longer term research agenda aimed at summarising scientific writing for lay readers using appropriate paraphrasing.
Convergence analysis of directed signed networks via an M-matrix approach

ABSTRACT This paper aims at solving convergence problems on directed signed networks with multiple nodes, where interactions among nodes are described by signed digraphs. The convergence analysis is achieved by matrix-theoretic and graph-theoretic tools, in which M-matrices play a central role. The fundamental digon sign-symmetry assumption upon signed digraphs can be removed with the proposed analysis approach. Furthermore, necessary and sufficient conditions are established for semi-positive and positive stabilities of Laplacian matrices of signed digraphs, respectively. A benefit of this result is that given strong connectivity, a directed signed network can achieve bipartite consensus (or state stability) if and only if the signed digraph associated with it is structurally balanced (or unbalanced). If the interactions between nodes are described by a signed digraph only with spanning trees, a directed signed network can achieve interval bipartite consensus (or state stability) if and only if the signed digraph contains a structurally balanced (or unbalanced) rooted subgraph. Simulations are given to illustrate the developed results by considering signed networks associated with digon sign-unsymmetric signed digraphs.
Deciding to Cross

Why are there so many unauthorized migrants in the United States? Using unique survey data collected in Mexico through the Mexican Migration Project, I develop and test a new decision-making model of unauthorized labor migration. The new model considers the economic motivations of prospective migrants, as well as their beliefs, attitudes, and social norms regarding U.S. immigration law and legal authorities. My findings show that perceptions of certainty of apprehension and severity of punishment are not significant determinants of the intent to migrate illegally; however, perceptions of availability of Mexican jobs and the dangers of border crossing are significant determinants of these intentions. In addition, individuals’ general legal attitudes, morality about violating U.S. immigration law, views about the legitimacy of U.S. authority, and norms about border crossing are significant determinants of the intent to migrate illegally. Perceptions of procedural justice are significantly related to beliefs in the legitimacy of U.S. authority, suggesting that, all else being equal, procedural fairness may produce greater deference to U.S. immigration law. Together, the results show that the decision to migrate illegally cannot be fully understood without considering an individual’s underlying values and norms.
Nonlinear Discriminative Data Visualization

Due to the tremendous increase of electronic information with respect to the size of data sets as well as dimensionality, visualiza- tion of high-dimensional data constitutes one of the key problems of data mining. Since embedding in lower dimensions necessarily includes a loss of information, methods to explicitly control the information kept by a specific visualization technique are highly desirable. The incorporation of supervised class information constitutes an important specific case. In this contribution we propose an extension of prototype-based local matrix learning by a charting technique which results in an efficient nonlinear di- mension reduction and discriminative visualization of a given labelled data manifold.
Measurement of absolute copy number variation of Glutathione S‐Transferase M1 gene by digital droplet PCR and association analysis in Tunisian Rheumatoid Arthritis population

The investigation of copy number variations (CNVs) analysis of candidate genes is currently an important research area in modulating human diseases. We aimed to quantify CNVs in glutathione S‐transferase M1 (GSTM1) gene and determine its genetic contribution in Tunisian rheumatoid arthritis (RA) and its subsets through an innovative technique for quantification.