Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of endogenous and exogenous electron donors and trichloroethylene oxidation toxicity on trichloroethylene oxidation by methanotrophic cultures from a groundwater aquifer

Trichloroethylene (TCE)-transforming aquifer methanotrophs were evaluated for the influence of TCE oxidation toxicity and the effect of reductant availability on TCE transformation rates during methane starvation. TCE oxidation at relatively low (6 mg liter-1) TCE concentrations significantly reduced subsequent methane utilization in mixed and pure cultures tested and reduced the number of viable cells in the pure culture Methylomonas sp. strain MM2 by an order of magnitude. Perchloroethylene, tested at the same concentration, had no effect on the cultures. Neither the TCE itself nor the aqueous intermediates were responsible for the toxic effect, and it is suggested that TCE oxidation toxicity may have resulted from reactive intermediates that attacked cellular macromolecules. During starvation, all methanotrophs tested exhibited a decline in TCE transformation rates, and this decline followed exponential decay. Formate, provided as an exogenous electron donor, increased TCE transformation rates in Methylomonas sp. strain MM2, but not in mixed culture MM1 or unidentified isolate, CSC-1. Mixed culture MM2 did not transform TCE after 15 h of starvation, but mixed cultures MM1 and MM3 did. The methanotrophs in mixed cultures MM1 and MM3, and the unidentified isolate CSC-1 that was isolated from mixed culture MM1 contained lipid inclusions, whereas the methanotrophs of mixed culture MM2 and Methylomonas sp. strain MM2 did not. It is proposed that lipid storage granules serve as an endogenous source of electrons for TCE oxidation during methane starvation.
Video Summarization Using Geometric Primitives

Video summarization is the process to extract informative events of a video and represent in the condensed form. The paper proposes a new method for extracting important contents of a video for summarization using geometric primitives, such as line segments, angles, and conic parts. The primitives have the capabilities to represent complex shapes and structures of objects in a video frame. Therefore, they are indeed powerful features to localize objects in complex environments. After localizing objects, a cost function is applied to measure the dissimilarity of locations of geometric primitives to detect the movement of objects between consecutive frames. After detecting the dissimilar geometric primitives, amount of object movements are calculated based on the number and length of each geometric primitives. Utilizing this information, each video frame is assigned a probability score to become a key frame. Finally, a set of key frames are selected as per user preference. The proposed approach is evaluated using BL-7F, Office, and Lobby datasets and obtained better performance than the intra-view results of the recently proposed state of the art GMM based method.
Flavored E-cigarette Use and Cigarette Smoking Reduction and Cessation—A Large National Study among Young Adult Smokers

ABSTRACT Background: E-cigarette use prevalence has increased drastically among young adult cigarette smokers in recent years. Objectives: This study seeks to understand which e-cigarette flavors—sweet and fruity or tobacco and menthol/mint—are more likely to be associated with smoking reduction and cessation among young adults. Methods: Longitudinal data (waves 1 and 2) of the Population Assessment of Tobacco and Health (PATH) Study from young adult (aged 18–34) cigarette smokers (n = 4,645) at wave 1 and current e-cigarette users (n = 844) at wave 2 were used. Univariate and multivariate regressions were conducted to examine the associations between past-year smoking reduction and cessation and current e-cigarette flavor use at wave 2. Results: At wave 2, 25.9% of respondents either reduced or quit smoking, and 6.7%, 5.2%, and 6.3% of them reported currently using e-cigarettes with tobacco/menthol (TM) flavors, one non-tobacco/non-menthol (NTM) flavor, and multiple NTM flavors, respectively. E-cigarette users with one (AOR = 2.5, p < 0.001) and multiple NTM flavors (AOR = 3.0, p < 0.001) were more likely to have reduced or quit smoking over the past year compared to non-e-cigarette users. NTM flavor use was positively associated with e-cigarette use of a higher frequency and larger amount. Conclusions: The positive association between past-year smoking reduction and cessation and current NTM flavored e-cigarette use may be explained by young adults' escalated e-cigarette use with NTM flavors. Public health professionals should prevent and reduce multiple tobacco use through enhanced education about the harm of vaping NTM flavors and by advising young adult smokers to quit tobacco altogether using evidence-based methods.
A Dynamic Trust Establishment and Management Framework for Wireless Sensor Networks

In this paper, we present a trust establishment and management framework for hierarchical wireless sensor networks. The wireless sensor network architecture we consider consists of a collection of sensor nodes, cluster heads and a base station arranged hierarchically. The framework encompasses schemes for establishing and managing trust between these different entities. We demonstrate that the proposed framework helps to minimize the memory, computation and communication overheads involved in trust management in wireless sensor networks. Our framework takes into account direct and indirect (group) trust in trust evaluation as well as the energy associated with sensor nodes in service selection. It also considers the dynamic aspect of trust by introducing a trust varying function which could be adjusted to give greater weight to the most recently obtained trust values in the trust calculation. The architecture also has the ability to deal with the inter-cluster movement of sensor nodes using a combination of certificate based trust and behaviour based trust.
Epidemiological links between tuberculosis cases identified twice as efficiently by whole genome sequencing than conventional molecular typing: A population-based study

Background Patients with Mycobacterium tuberculosis isolates sharing identical DNA fingerprint patterns can be epidemiologically linked. However, municipal health services in the Netherlands are able to confirm an epidemiological link in only around 23% of the patients with isolates clustered by the conventional variable number of tandem repeat (VNTR) genotyping. This research aims to investigate whether whole genome sequencing (WGS) is a more reliable predictor of epidemiological links between tuberculosis patients than VNTR genotyping. Methods VNTR genotyping and WGS were performed in parallel on all Mycobacterium tuberculosis complex isolates received at the Netherlands National Institute for Public Health and the Environment in 2016. Isolates were clustered by VNTR when they shared identical 24-loci VNTR patterns; isolates were assigned to a WGS cluster when the pair-wise genetic distance was ≤ 12 single nucleotide polymorphisms (SNPs). Cluster investigation was performed by municipal health services on all isolates clustered by VNTR in 2016. The proportion of epidemiological links identified among patients clustered by either method was calculated. Results In total, 535 isolates were genotyped, of which 25% (134/535) were clustered by VNTR and 14% (76/535) by WGS; the concordance between both typing methods was 86%. The proportion of epidemiological links among WGS clustered cases (57%) was twice as common than among VNTR clustered cases (31%). Conclusion When WGS was applied, the number of clustered isolates was halved, while all epidemiologically linked cases remained clustered. WGS is therefore a more reliable tool to predict epidemiological links between tuberculosis cases than VNTR genotyping and will allow more efficient transmission tracing, as epidemiological investigations based on false clustering can be avoided.
Association of DDX58 177 C > T polymorphism with decreased risk of Epstein–Barr virus-related nodular sclerosis classical Hodgkin lymphoma

Abstract Classical Hodgkin lymphoma (cHL) is frequently related to Epstein–Barr virus (EBV) infection. Its malignant capacity is attributed to disruption of an EBV-host balance influenced by environmental and genetic drivers. EBV structures activate Type I interferon (IFN) pathway of the innate immunity, therefore, genetic polymorphisms could influence this response. We explored the impact of four single nucleotide polymorphisms (SNPs) on EBV-associated cHL susceptibility. Toll-like receptors 9 (TLR9_rs5743836), and 3 (TLR3_rs3775291), Interleukin-28B (IL28B_rs12979860), and DEAD-box polypeptide 58 (DDX58_rs10813831) were genotyped in 73 EBV-positive and 106 EBV-negative cHL patients and 396 controls. Only DDX58_rs10813831 T-allele was decreased among EBV-positive cHL compared to controls. A stratified analysis in EBV-positive cHL showed that the reduced rate was associated with younger age and nodular sclerosis. In conclusion, DDX58_rs10813831 T-allele may be associated with a reduced risk of nodular sclerosis EBV-related cHL, which suggests a role for RIG-I (retinoic acid-inducible gene I), encoded by DDX58, in these cases.
Beat by beat: Classifying cardiac arrhythmias with recurrent neural networks

With tens of thousands of electrocardiogram (ECG) records processed by mobile cardiac event recorders every day, heart rhythm classification algorithms are an important tool for the continuous monitoring of patients at risk. We utilise an annotated dataset of 12,186 single-lead ECG recordings to build a diverse ensemble of recurrent neural networks (RNNs) that is able to distinguish between normal sinus rhythms, atrial fibrillation, other types of arrhythmia and signals that are too noisy to interpret. In order to ease learning over the temporal dimension, we introduce a novel task formulation that harnesses the natural segmentation of ECG signals into heartbeats to drastically reduce the number of time steps per sequence. Additionally, we extend our RNNs with an attention mechanism that enables us to reason about which heartbeats our RNNs focus on to make their decisions. Through the use of attention, our model maintains a high degree of interpretability, while also achieving state-of-the-art classification performance with an average F1 score of 0.79 on an unseen test set (n=3,658).
Advanced Passivity-Based Control for a Fuel Cell/Super-Capacitor Hybrid Power System

To solve the converters coordination problem of a fuel cell/super capacitor hybrid power system, an advanced passivity-based control is proposed in this paper. The Interconnection and Damping Assignment Passivity Based Control (IDA-PBC) is applied to design the controller. This nonlinear controller considers the state of charge of super capacitor and achieves the stability of the whole closed-loop system. Its feasibility for an electrical vehicle is proven by the simulation results and the comparison with the previous method.
Two-dimensional Thermomechanical Analysis and Optimization of Functionally Graded Materials

Summary In this paper, we study the two-dimensional volume fraction optimization of heat resisting metal/ceramic functionally graded materials (FGMs). The plane stress static thermoelastic behavior of a FGM is analyzed using the element-free Galerkin method. The effective material properties of the twophase FGM is estimated using the Mori-Tanaka and self consistent schemes. A genetic algorithm optimization procedure is used to determine the ceramic volume fraction distribution that would minimize the peak effective stress.
Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections

Significance In many infections, multiple microbial species are present simultaneously. Such polymicrobial infections can be viewed as small microbial ecosystems. Do bacteria in these communities interact with each other? If so, do these interactions affect the stability of the ecosystem, in particular, when antibiotics are present? We focus on urinary tract infections and demonstrate that there are ample ecological interactions between different bacterial species, both in the presence and absence of antibiotics. We further show that they crucially affect ecosystem stability and resilience to environmental perturbations such as antibiotics. Understanding the nature of these polymicrobial communities can point toward ways of disrupting infection ecosystems, which could potentially be used as a new strategy to eradicate infective communities. Polymicrobial infections constitute small ecosystems that accommodate several bacterial species. Commonly, these bacteria are investigated in isolation. However, it is unknown to what extent the isolates interact and whether their interactions alter bacterial growth and ecosystem resilience in the presence and absence of antibiotics. We quantified the complete ecological interaction network for 72 bacterial isolates collected from 23 individuals diagnosed with polymicrobial urinary tract infections and found that most interactions cluster based on evolutionary relatedness. Statistical network analysis revealed that competitive and cooperative reciprocal interactions are enriched in the global network, while cooperative interactions are depleted in the individual host community networks. A population dynamics model parameterized by our measurements suggests that interactions restrict community stability, explaining the observed species diversity of these communities. We further show that the clinical isolates frequently protect each other from clinically relevant antibiotics. Together, these results highlight that ecological interactions are crucial for the growth and survival of bacteria in polymicrobial infection communities and affect their assembly and resilience.
Electrical properties of polyaniline–polystyrene blends above the percolation threshold

Blends of conductive polymers with classical ones can exhibit good mechanical properties and good electrical conductivity and deserve great attention for application in electronic industrial technology. Conductive polyaniline solutions have been chemically prepared using bis(2-ethyl hexyl)hydrogen phosphate (DiOHP) as the dopant chemical species. The codissolution method leads to conductive polyaniline–polystyrene (PANI–PSt) composites with good mechanical properties. The dependence of electrical conductivity on the volume fraction of PANI in the blend is found to be characteristic of a percolation system. Electrical conductivity and thermoelectric power measurements are interpreted on the basis of hopping mechanisms between polaronic clusters. © 1998 John Wiley & Sons, Inc. J Appl Polym Sci 67:1205–1208, 1998
Influence of a Technogenic Silicate Product Admixtures on Silicate Concrete Properties

The influence of three types of technogenical products (cement dust – waste of cement production, autoclaved cellular concrete waste and condensate from the autoclaves) on silicate concrete properties was analysed in this paper. Use of these products is limited and the condensate is practically unused for production. It was determined that the mixture of water and condensate (1 : 1) could be used to slake the silicate mixture, then the compressive strength of the silicate concrete increases by 15%, and additionally including 3 wt. % of cement dust or 5 wt. % of porous concrete waste, the silicate concrete compressive strength increases from 21 % to 26 %.
Context Shapes Social Judgments of Positive Emotion Suppression and Expression

It is generally considered socially undesirable to suppress the expression of positive emotion. However, previous research has not considered the role that social context plays in governing appropriate emotion regulation. We investigated a context in which it may be more appropriate to suppress than express positive emotion, hypothesizing that positive emotion expressions would be considered inappropriate when the valence of the expressed emotion (i.e., positive) did not match the valence of the context (i.e., negative). Six experiments (N = 1,621) supported this hypothesis: when there was a positive emotion-context mismatch, participants rated targets who suppressed positive emotion as more appropriate, and evaluated them more positively than targets who expressed positive emotion. This effect occurred even when participants were explicitly made aware that suppressing targets were experiencing mismatched emotion for the context (e.g., feeling positive in a negative context), suggesting that appropriate emotional expression is key to these effects. These studies are among the first to provide empirical evidence that social costs to suppression are not inevitable, but instead are dependent on context. Expressive suppression can be a socially useful emotion regulation strategy in situations that call for it.
Mutagenesis of Dengue Virus Protein NS2A Revealed a Novel Domain Responsible for Virus-Induced Cytopathic Effect and Interactions between NS2A and NS2B Transmembrane Segments

ABSTRACT The NS2A protein of dengue virus (DENV) has eight predicted transmembrane segments (pTMS1 to -8) and participates in RNA replication, virion assembly, and host antiviral response. However, the roles of specific amino acid residues within the pTMS regions of NS2A during the viral life cycle are not clear. Here, we explore the function of DENV NS2A by introducing a series of alanine substitutions into the N-terminal half (pTMS1 to -4) of the protein in the context of a DENV infectious clone or subgenomic replicon. Six NS2A mutants (NM5, -7, -9, and -17 to -19) around pTMS1 and -2 displayed a novel phenotype showing a >1,000-fold reduction in virus yield, an absence of plaque formation despite wild-type-like replicon activity, and infectious-virus-like particle yields. HEK-293 cells infected with the six NS2A mutant viruses failed to cause a virus-induced cytopathic effect (CPE) by MitoCapture staining, cell proliferation, and lactate dehydrogenase release assays. Sequencing analyses of pseudorevertant viruses derived from lethal-mutant viruses revealed two consensus reversion mutations, leucine to phenylalanine at codon 181 (L181F) within pTMS7 of NS2A and isoleucine to threonine at codon 114 (I114T) within NS2B. The introduction of an NS2A-L181F mutation into the lethal (NM15, -16, -25, and -33) and CPE-defective (NM7, -9, and -19) mutants substantially rescued virus infectivity and virus-induced CPE, respectively, whereas the NS2B-L114T mutation rescued the NM16, -25, and -33 mutants. In conclusion, the results revealed the essential roles of the N-terminal half of NS2A in RNA replication and virus-induced CPE. Intramolecular interactions between pTMSs of NS2A and intermolecular interactions between the NS2A and NS2B proteins were also implicated. IMPORTANCE The characterization of the N-terminal (current study) and C-terminal halves of DENV NS2A is the most comprehensive mutagenesis study to date to investigate the function of NS2A during the flaviviral life cycle. A novel region responsible for virus-induced cytopathic effect (CPE) within pTMS1 and -2 of DENV NS2A was identified. Revertant genetics studies implied unexpected relationships between various pTMSs of DENV NS2A and NS2B. These results provide comprehensive information regarding the functions of DENV NS2A and the specific amino acids and transmembrane segments responsible for these functions. The positions and properties of the rescuing mutations were also revealed, providing important clues regarding the manner in which intramolecular or intermolecular interactions between the pTMSs of NS2A and NS2B regulate virus replication, assembly/secretion, and virus-induced CPE. These results expand the understanding of flavivirus replication. The knowledge may also facilitate studies of pathogenesis and novel vaccine and antiflaviviral drug development.
Transcriptomic Profiles of Brain Provide Insights into Molecular Mechanism of Feed Conversion Efficiency in Crucian Carp (Carassius auratus)

Feed efficiency is an economically crucial trait for cultured animals, however, progress has been scarcely made in the genetic analyses of feed conversion efficiency (FCE) in fish because of the difficulties in measurement of trait phenotypes. In the present investigation, we present the first application of RNA sequencing (RNA-Seq) combined with differentially expressed genes (DEGs) analysis for identification of functional determinants related to FCE at the gene level in an aquaculture fish, crucian carp (Carassius auratus). Brain tissues of six crucian carp with extreme FCE performances were subjected to transcriptome analysis. A total of 544,612 unigenes with a mean size of 644.38 bp were obtained from Low- and High-FCE groups, and 246 DEGs that may be involved in FCE traits were identified in these two groups. qPCR confirmed that genes previously identified as up- or down-regulated by RNA-Seq were effectively up- or down-regulated under the studied conditions. Thirteen key genes, whose functions are associated with metabolism (Dgkk, Mgst3 and Guk1b), signal transduction (Vdnccsa1b, Tgfα, Nr4a1 and Tacr2) and growth (Endog, Crebrtc2, Myh7, Myh1, Myh14 and Igfbp7) were identified according to GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) annotations. Our novel findings provide useful pathway information and candidate genes for future studies of genetic mechanisms underlying FCE in crucian carp.
Surgery for Glioblastoma in Light of Molecular Markers: Impact of Resection and MGMT Promoter Methylation in Newly Diagnosed IDH-1 Wild-Type Glioblastomas

BACKGROUND Previous studies addressing the influence of surgery on the outcome of patients with glioblastomas (GBM) have not addressed molecular markers. The value of surgery versus the tumor's major biological markers remains unclear. OBJECTIVE We investigate the extent of resection as a prognosticator for patients with newly diagnosed primary GBM with the incorporation of molecular diagnostics as per the updated WHO 2016 diagnostic criteria for GBM. METHODS Patients with newly diagnosed GBM who underwent resection were prospectively included within a database. We analyzed patients with newly diagnosed GBM and excluded patients who presented with IDH1 R132H mutations. Gross total resection (GTR) was defined as complete removal of enhancing disease. RESULTS One hundred seventy-five patients were included within the analysis. One hundred four patients (59.4%) had GTR, 71 patients (40.6%) had subtotal or partial resection. Eighty patients (45.7%) displayed O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation, 95 patients (54.3%) showed no MGMT promoter methylation. In Cox regression analysis, MGMT promoter methylation (hazard ratio [HR] 1.55; 95% confidence interval [CI], 1.01-2.19; P = .0133) and GTR (HR 1.48; 95% CI, 1.06-2.07; P = .0206) were significantly associated with favorable progression-free survival. MGMT promoter methylation (HR 2.13; 95% CI, 1.45-3.12; P = .0001) and GTR (HR 1.81; 95% CI, 1.24-2.63; P = .002) were associated with favorable overall survival (OS). Of other risk factors analyzed, age (>60 vs ≤ 60 yr) was significantly associated with progression-free survival (HR 1.60; 95% CI, 1.14-2.24; P = .006) and OS (HR 2.19; 95% CI, 1.51-3.19; P < .0001). CONCLUSION GTR and MGMT promoter methylation are independent prognosticators for improved overall and progression-free survival in a homogeneous cohort of newly diagnosed patients with IDH wild-type glioblastoma.