Miracle-dz/UniFAR-FTUs huggingface dataset:
Reducing Redundancy in Keyword Query Processing on Graph Databases

In this paper, we propose a new approach to reducing redundancy in the answers to a keyword query over large graph databases. Aiming to generate query results which are not only relevant but also has diverse structures and content nodes, we propose a method to find top-k answer sub-trees which should be in reduced forms and duplication-free in regard to the set of content nodes. To process keyword queries efficiently over large graph data, we suggest an efficient indexing scheme on the most relevant paths from nodes to keyword terms in the graph. We present a top-k query processing algorithm which exploits the pre-constructed indexes to search for a set of most relevant and non-redundant answers. We also provide a state space search algorithm to find most relevant duplication-free answers in an efficient way. We show effectiveness and efficiency of the proposed approach in comparison with the previous methods using extensive experiments on real graph datasets.
Buruli Ulcer: Review of a Neglected Skin Mycobacterial Disease

ABSTRACT Buruli ulcer is caused by Mycobacterium ulcerans. This neglected disease occurs in scattered foci around the world, with a higher concentration of cases in West Africa. The mycobacteria produce mycolactones that cause tissue necrosis. The disease presents as a painless skin nodule that ulcerates as necrosis expands. Finding acid-fast bacilli in smears or histopathology, culturing the mycobacteria, and performing M. ulcerans PCR in presumptive cases confirm the diagnosis. Medical treatment with oral rifampin and intramuscular streptomycin or oral treatment with rifampin plus clarithromycin for 8 weeks is supported by the World Health Organization. This review summarizes the epidemiology, pathogenesis, clinical presentation, diagnostic tests, and advances in treatment.
Finite Element Modelling in Premolar Teeth

A three-dimensional finite element model was developed using the ABAQUS code to characterize dental systems in their different functional conditions, geometry and loading modes.The outputs of the model were used to evaluate quantitatively the magnitude and distribution of the stress-strain-displacement relations in sound (drilled and enamel crown) and restored with prefabricated intrarradicular posts (conical and cylindrical) premolar teeth specimens.Under the same loading and boundary conditions, differences in stresses, displacements and elastic strains were observed for drilled, enamel crown, conical and cylindrical post teeth specimens. It was found that the cylindrical glass fiber post geometry minimizes much better the stress, displacement and elastic strain magnitude in premolar teeth.The results indicate that the finite element methodology is adequate and convenient for stress, displacement and strain assessment in orthodontics.
Molecular basis and function of voltage-gated K+ channels in pulmonary arterial smooth muscle cells.

K+-channel activity-mediated alteration of the membrane potential and cytoplasmic free Ca2+ concentration ([Ca2+]cyt) is a pivotal mechanism in controlling pulmonary vasomotor tone. By using combined approaches of patch clamp, imaging fluorescent microscopy, and molecular biology, we examined the electrophysiological properties of K+ channels and the role of different K+ currents in regulating [Ca2+]cytand explored the molecular identification of voltage-gated K+(KV)- and Ca2+-activated K+(KCa)-channel genes expressed in pulmonary arterial smooth muscle cells (PASMC). Two kinetically distinct KV currents [ I K(V)], a rapidly inactivating (A-type) and a noninactivating delayed rectifier, as well as a slowly activated KCa current [ I K(Ca)] were identified. I K(V) was reversibly inhibited by 4-aminopyridine (5 mM), whereas I K(Ca) was significantly inhibited by charybdotoxin (10-20 nM). K+ channels are composed of pore-forming α-subunits and auxiliary β-subunits. Five KV-channel α-subunit genes from the Shaker subfamily (KV1.1, KV1.2, KV1.4, KV1.5, and KV1.6), a KV-channel α-subunit gene from the Shab subfamily (KV2.1), a KV-channel modulatory α-subunit (KV9.3), and a KCa-channel α-subunit gene ( rSlo), as well as three KV-channel β-subunit genes (KVβ1.1, KVβ2, and KVβ3) are expressed in PASMC. The data suggest that 1) native K+ channels in PASMC are encoded by multiple genes; 2) the delayed rectifier I K(V)may be generated by the KV1.1, KV1.2, KV1.5, KV1.6, KV2.1, and/or KV2.1/KV9.3 channels; 3) the A-type I K(V) may be generated by the KV1.4 channel and/or the delayed rectifier KV channels (KV1 subfamily) associated with β-subunits; and 4) the I K(Ca) may be generated by the rSlo gene product. The function of the KV channels plays an important role in the regulation of membrane potential and [Ca2+]cytin PASMC.
The Mercurian magma ocean , first crust , and implications for planetary formation mechanisms

The size of the Mercurian core and the low ferrous iron bearing silicate content of its crust offer constraints on formation models for the planet. Here we consider a bulk composition that allows endogenous formation of the planet's large core, and by processing the mantle through a magma ocean, would produce a low-iron crust. More Earth-like bulk compositions require silicate removal, perhaps by a giant impact, to create the planet's large core fraction. The earliest crusts expected in a giant impact scenario are discussed in comparison to the endogenous model. We find that the endogenous model can produce a large core with either a plagioclase flotation crust or a low-iron magmatic crust. For the giant impact model, in the absence of a plagioclase flotation crust, the impact may be constrained to occur within about 300,000 years of the planet's initial fractionating magma ocean, at which time the giant impact can remove most of the silicate iron oxide budget of the planet before gravitational overturn carries it into the deep planetary interior. Thus a specific bulk composition is required to make Mercury endogenously, but specific timing of events is required to make it exogenously through giant impact. Measurements taken by the MESSENGER mission, when compared to predictions given here, may help resolve Mercury's formation process.
Development of Novel Octanoyl Chitosan Nanoparticles for Improved Rifampicin Pulmonary Delivery: Optimization by Factorial Design

A novel hydrophobic chitosan derivative, octanoyl chitosan (OC) with improved organic solubility was synthesized, characterized, and employed for the preparation of rifampicin (Rif) encapsulated nanoparticle formulations for pulmonary delivery. OC was characterized to confirm acyl group substitution and cytotoxicity in A549 epithelial lung cells. OC nanoparticles were produced by the double emulsion solvent evaporation technique without cross-linking and characterized for particle size distribution, morphology, crystallinity, thermal stability, aerosol delivery, and drug release rate. OC was successfully synthesized with substitution degree of 44.05 ± 1.75%, and solubility in a range of organic solvents. Preliminary cytotoxicity studies of OC showed no effect on cell viability over a period of 24 h on A549 cell lines. OC nanoparticles were optimized using a 32 full factorial design. An optimized batch of OC nanoparticles, smooth and spherical in morphology, had mean hydrodynamic diameter of 253 ± 19.06 nm (PDI 0.323 ± 0.059) and entrapment efficiency of 64.86 ± 7.73% for rifampicin. Pulmonary deposition studies in a two-stage impinger following aerosolization of nanoparticles from a jet nebulizer gave a fine particle fraction of 43.27 ± 4.24%. In vitro release studies indicated sustained release (73.14 ± 3.17%) of rifampicin from OC nanoparticles over 72 h, with particles demonstrating physical stability over 2 months. In summary, the results confirmed the suitability of the developed systems for pulmonary delivery of drugs with excellent aerosolization properties and sustained-release characteristics.
Emergent Oscillations in Networks of Stochastic Spiking Neurons

Networks of neurons produce diverse patterns of oscillations, arising from the network's global properties, the propensity of individual neurons to oscillate, or a mixture of the two. Here we describe noisy limit cycles and quasi-cycles, two related mechanisms underlying emergent oscillations in neuronal networks whose individual components, stochastic spiking neurons, do not themselves oscillate. Both mechanisms are shown to produce gamma band oscillations at the population level while individual neurons fire at a rate much lower than the population frequency. Spike trains in a network undergoing noisy limit cycles display a preferred period which is not found in the case of quasi-cycles, due to the even faster decay of phase information in quasi-cycles. These oscillations persist in sparsely connected networks, and variation of the network's connectivity results in variation of the oscillation frequency. A network of such neurons behaves as a stochastic perturbation of the deterministic Wilson-Cowan equations, and the network undergoes noisy limit cycles or quasi-cycles depending on whether these have limit cycles or a weakly stable focus. These mechanisms provide a new perspective on the emergence of rhythmic firing in neural networks, showing the coexistence of population-level oscillations with very irregular individual spike trains in a simple and general framework.
Pancreatic trypsinogen I expression during cell growth and differentiation of two human colon carcinoma cells

FRANÇOISE BERNARD-PERRONE,1 JACQUELINE CARRERE,2 WANDA RENAUD,3 CHRISTINE MORISCOT,3 KARINE THOREUX,1 PATRICE BERNARD,1 ALAIN SERVIN,4 DANIEL BALAS,1 AND FRANÇOISE SENEGAS-BALAS1 1Groupe de Recherche sur la Trophicité et le Vieillissement, Faculté de Médecine, 06107 Nice Cedex 2; 3Groupe de Recherche sur les Glandes Exocrines, 13385 Marseille Cedex; 2Hopital Renée Sabran, Giens, 83406 Hyères Cedex; and 4Contrat Jeune Formation, Institut National de la Santé et de la Recherche Médicale 94-07, Unité de Formation et de Recherche-Sciences-Pharmacie, Paris XI, 92296 Chatenay-Malabry Cedex, France
Using Neural Networks to Detect Line Outages from PMU Data

We propose an approach based on neural networks and the AC power flow equations to identify single- and double- line outages in a power grid using the information from phasor measurement unit sensors (PMUs). Rather than inferring the outage from the sensor data by inverting the physical model, our approach uses the AC model to simulate sensor responses to all outages of interest under multiple demand and seasonal conditions, and uses the resulting data to train a neural network classifier to recognize and discriminate between different outage events directly from sensor data. After training, real-time deployment of the classifier requires just a few matrix-vector products and simple vector operations. These operations can be executed much more rapidly than inversion of a model based on AC power flow, which consists of nonlinear equations and possibly integer / binary variables representing line outages, as well as the variables representing voltages and power flows. We are motivated to use neural network by its successful application to such areas as computer vision and natural language processing. Neural networks automatically find nonlinear transformations of the raw data that highlight useful features that make the classification task easier. We further consider the problem of classifying outages from sensors placed at only a subset of the buses, describing a principled way to choose sensor locations and showing that highly accurate classification can be achieved from a restricted set of measurements.
Self-Reported Risk and Delinquent Behavior and Problem Behavioral Intention in Hong Kong Adolescents: The Role of Moral Competence and Spirituality

Based on the six-wave data collected from Grade 7 to Grade 12 students (N = 3,328 at Wave 1), this pioneer study examined the development of problem behaviors (risk and delinquent behavior and problem behavioral intention) and the predictors (moral competence and spirituality) among adolescents in Hong Kong. Individual growth curve models revealed that while risk and delinquent behavior accelerated and then slowed down in the high school years, adolescent problem behavioral intention slightly accelerated over time. After controlling the background socio-demographic factors, moral competence and spirituality were negatively associated with risk and delinquent behavior as well as problem behavioral intention across all waves as predicted. Regarding the rate of change in the outcome measures, while the initial level of spirituality was positively linked to the growth rate of risk and delinquent behavior, the initial level of moral competence was negatively associated with the growth rate of problem behavioral intention. The theoretical and practical implications of the present findings are discussed with reference to the role of moral competence and spirituality in the development of adolescent problem behavior.
Regulation of apolipoprotein A-I gene expression in Hep G2 cells depleted of Cu by cupruretic tetramine.

Studies were designed to examine the regulation of apolipoprotein (apo) A-I gene expression in Cu-depleted Hep G2 cells. The cupruretic chelator N, N'-bis(2-aminoethyl)-1,3-propanediamine ⋅ 4 HCl (2,3,2-tetramine or TETA) was used to maintain a 77% reduction in cellular Cu in Hep G2 cells. After two passages of TETA treatment, the relative abundance of apoA-I mRNA was elevated 52%. In TETA-treated cells, the rate of apoA-I mRNA decay measured by an actinomycin D chase study was accelerated 108%, and the synthesis of apoA-I mRNA determined by a nuclear runoff assay was enhanced 2.5-fold in TETA-treated cells. All of those changes could be reverted toward the control values with Cu supplementation for only 2 days. In transient transfection assays, a 26.7% increase in chloramphenicol O-acetyltransferase (CAT) activity for the reporter construct -256AI-CAT was observed in the treated cells. However, the ability of apoA-I regulatory protein 1 (ARP-1) to repress the CAT activity was not affected by the depressed Cu status. In addition, gel retardation experiments demonstrated that Cu depletion enhanced the binding of hepatocyte nuclear factor 4 (HNF-4) and other undefined nuclear factors to oligonucleotides containing site A, one of three regulatory sites of the apoA-I gene promoter. Moreover, the relative abundance of HNF-4 mRNA was increased 58% in the Cu-depleted cells. Thus the observed increase in apoA-I gene transcription may be mediated mostly by an elevated level of the regulatory factor, HNF-4. In summary, the present findings established the mechanism by which a depressed cellular Cu status can enhance apoA-I mRNA production and subsequently increase apoA-I synthesis.
On the supergravity evaluation of Wilson loop correlators in confining theories

We explicitly show the area law behavior of a circular Wilson loop in confining theories from supergravity. We calculate the correlator of two Wilson loops from supergravity in confining backgrounds. We find that it is dominated by an exchange of a ``scalarball'' that is lighter than the glueballs. We interpret these results in terms of the meson-meson potential in such theories.
Evacuating an Equilateral Triangle in the Face-to-Face Model

Consider k robots initially located at the centroid of an equilateral triangle T of sides of length one. The goal of the robots is to evacuate T through an exit at an unknown location on the boundary of T. Each robot can move anywhere in T independently of other robots with maximum speed one. The objective is to minimize the evacuation time, which is defined as the time required for all k robots to reach the exit. We consider the face-to-face communication model for the robots: a robot can communicate with another robot only when they meet in T. In this paper, we give upper and lower bounds for the face-to-face evacuation time by k robots. We show that for any k, any algorithm for evacuating k >= 1 robots from T requires at least sqrt(3) time. This bound is asymptotically optimal, as we show that a straightforward strategy of evacuation by k robots gives an upper bound of sqrt(3) + 3/k. For k = 3, 4, 5, 6, we show significant improvements on the obvious upper bound by giving algorithms with evacuation times of 2.0887, 1.9816, 1.876, and 1.827, respectively. For k = 2 robots, we give a lower bound of 1 + 2/sqrt(3) ~= 2.154, and an algorithm with upper bound of 2.3367 on the evacuation time.
Regional glycerol and free fatty acid metabolism before and after meal ingestion.

We measured splanchnic and leg glycerol [and free fatty acid (FFA)] uptake and release in 11 healthy volunteers before and after meal ingestion to assess whether regional FFA-to-glycerol release ratios mirror systemic release ratios. Basal splanchnic triglyceride release was also assessed. Although basal splanchnic glycerol uptake (111 ± 18 μmol/min) accounted for most of systemic glycerol rate of appearance (156 ± 20 μmol/min), leg glycerol uptake was also noted. The basal, systemic FFA-to-glycerol release ratio was less (2.6 ± 0.2, P < 0.05) than the splanchnic ratio of 6.1 ± 1.3, and the leg FFA-to-glycerol release ratio under fed conditions was less than the systemic ratio (0.9 ± 0.1 vs. 1.6 ± 0.2, respectively, P< 0.05). Basal splanchnic triglyceride production rates were 74 ± 20 μmol/min, which could produce equimolar amounts of glycerol in the peripheral circulation via lipoprotein lipase action. In summary, 1) regional FFA-to-glycerol release ratios do not mirror systemic ratios, 2) leg glycerol uptake occurs in humans, and 3) splanchnic triglyceride production rates are substantial relative to systemic glycerol appearance. Glycerol appearance rates may not be a quantitative index of whole body lipolysis.
Effect of glucose supplementation on appetite and the pyloric motor response to intraduodenal glucose and lipid.

The effects of different macronutrients on appetite and pyloric motility and the impact of short-term dietary glucose supplementation on these responses were evaluated. Ten males (aged 19-38 yr) received isocaloric (2.9 kcal/min) intraduodenal infusions of glucose and lipid while antropyloroduodenal motility and appetite were assessed by manometry and visual analog scales, respectively. Effects of each intraduodenal nutrient on appetite and motility were evaluated before and after 7 days of dietary supplementation with glucose (400 g daily). Initially, both nutrients caused a similar rise in pyloric tone, but intraduodenal lipid was a more potent stimulus of phasic pyloric motility ( P = 0.05) and suppressed appetite more ( P = 0.013) than intraduodenal glucose. After dietary glucose supplementation, the increase in pyloric tone during intraduodenal glucose was attenuated. Although intraduodenal lipid remained a more potent stimulant of phasic pyloric motility ( P = 0.016), it no longer decreased appetite. We conclude that in healthy young males 1) intraduodenal infusion of lipid is a more potent stimulus of phasic pyloric motility and suppresses appetite more than intraduodenal glucose and 2) dietary glucose supplementation alters both the appetite suppressant effect of intraduodenal lipid and the pyloric motor response to intraduodenal glucose infusion.
Human Cytomegalovirus Immediate Early Interaction with Host Nuclear Structures: Definition of an Immediate Transcript Environment

The development of an induced transcript environment was investigated at the supramolecular level through comparative localization of the human cytomegalovirus immediate early (IE) transcripts and specific nuclear domains shortly after infection. Compact aggregates of IE transcripts form only adjacent to nuclear domain 10 (ND10), and the viral protein IE86 accumulates exclusively juxtaposed to the subpopulation of ND10 with transcripts. The stream of transcripts is funneled from ND10 into the spliceosome assembly factor SC35 domain through the accumulation of IE86 protein, which recruits some components of the basal transcription machinery. Concomitantly the IE72 protein binds to ND10 and later disperses them. The domain containing the zinc finger region of IE72 is essential for this dispersal. Positional analysis of proteins IE86 and IE72, IE transcripts, ND10, the spliceosome assembly factor SC35, and basal transcription factors defines spatially and temporally an immediate transcript environment, the basic components of which exist in the cell before viral infection, providing the structural environment for the virus to usurp.
Single-molecule nanopore enzymology

Biological nanopores are a class of membrane proteins that open nanoscale water conduits in biological membranes. When they are reconstituted in artificial membranes and a bias voltage is applied across the membrane, the ionic current passing through individual nanopores can be used to monitor chemical reactions, to recognize individual molecules and, of most interest, to sequence DNA. In addition, a more recent nanopore application is the analysis of single proteins and enzymes. Monitoring enzymatic reactions with nanopores, i.e. nanopore enzymology, has the unique advantage that it allows long-timescale observations of native proteins at the single-molecule level. Here, we describe the approaches and challenges in nanopore enzymology. This article is part of the themed issue ‘Membrane pores: from structure and assembly, to medicine and technology’.
The Arabidopsis leaf transcriptome reveals distinct but also overlapping responses to colonization by phyllosphere commensals and pathogen infection with impact on plant health.

Plants are colonized by a variety of bacteria, most of which are not pathogenic. Currently, the plant responses to phyllosphere commensals or to pathogen infection in the presence of commensals are not well understood. Here, we examined the transcriptional response of Arabidopsis thaliana leaves to colonization by common commensal bacteria in a gnotobiotic system using RNA sequencing and conducted plant mutant assays. Arabidopsis responded differently to the model bacteria Sphingomonas melonis Fr1 (S.Fr1) and Methylobacterium extorquens PA1 (M.PA1). Whereas M.PA1 only marginally affected the expression of plant genes (< 10), S.Fr1 colonization changed the expression of almost 400 genes. For the latter, genes related to defense responses were activated and partly overlapped with those elicited by the pathogen Pseudomonas syringae DC3000 (Pst). As S.Fr1 is able to mediate plant protective activity against Pst, we tested plant immunity mutants and found that the pattern-recognition co-receptor mutant bak1/bkk1 showed attenuated S.Fr1-dependent plant protection. The experiments demonstrate that the plant responds differently to members of its natural phyllosphere microbiota. A subset of commensals trigger expression of defense-related genes and thereby may contribute to plant health upon pathogen encounter.
Model‐Based Meta‐Analysis for Multiple Myeloma: A Quantitative Drug‐Independent Framework for Efficient Decisions in Oncology Drug Development

The failure rate for phase III trials in oncology is high; quantitative predictive approaches are needed. We developed a model‐based meta‐analysis (MBMA) framework to predict progression‐free survival (PFS) from overall response rates (ORR) in relapsed/refractory multiple myeloma (RRMM), using data from seven phase III trials. A Bayesian analysis was used to predict the probability of technical success (PTS) for achieving desired phase III PFS targets based on phase II ORR data. The model demonstrated a strongly correlated (R2 = 0.84) linear relationship between ORR and median PFS. As a representative application of the framework, MBMA predicted that an ORR of ∼66% would be needed in a phase II study of 50 patients to achieve a target median PFS of 13.5 months in a phase III study. This model can be used to help estimate PTS to achieve gold‐standard targets in a target product profile, thereby enabling objectively informed decision‐making.