Miracle-dz/UniFAR-FTUs huggingface dataset:
Ethanol and Other Short-Chain Alcohols Inhibit NLRP3 Inflammasome Activation through Protein Tyrosine Phosphatase Stimulation

Immunosuppression is a major complication of alcoholism that contributes to increased rates of opportunistic infections and sepsis in alcoholics. The NLRP3 inflammasome, a multiprotein intracellular pattern recognition receptor complex that facilitates the cleavage and secretion of the proinflammatory cytokines IL-1β and IL-18, can be inhibited by ethanol, and we sought to better understand the mechanism through which this occurs and whether chemically similar molecules exert comparable effects. We show that ethanol can specifically inhibit activation of the NLRP3 inflammasome, resulting in attenuated IL-1β and caspase-1 cleavage and secretion, as well as diminished apoptosis-associated speck-like protein containing a CARD (ASC) speck formation, without affecting potassium efflux, in a mouse macrophage cell line (J774), mouse bone marrow–derived dendritic cells, mouse neutrophils, and human PBMCs. The inhibitory effects on the Nlrp3 inflammasome were independent of γ-aminobutyric acid A receptor activation or N-methyl-d-asparate receptor inhibition but were associated with decreased oxidant production. Ethanol treatment markedly decreased cellular tyrosine phosphorylation, whereas administration of the tyrosine phosphatase inhibitor sodium orthovanadate prior to ethanol restored tyrosine phosphorylation and IL-1β secretion subsequent to ATP stimulation. Furthermore, sodium orthovanadate–induced phosphorylation of ASC Y144, necessary and sufficient for Nlrp3 inflammasome activation, and secretion of phosphorylated ASC were inhibited by ethanol. Finally, multiple alcohol-containing organic compounds exerted inhibitory effects on the Nlrp3 inflammasome, whereas 2-methylbutane (isopentane), the analogous alkane of the potent inhibitor isoamyl alcohol (isopentanol), did not. Our results demonstrate that ethanol antagonizes the NLRP3 inflammasome at an apical event in its activation through the stimulation of protein tyrosine phosphatases, an effect shared by other short-chain alcohols.
Isolation and expression of the homeobox gene Gbx1 during mouse development

In zebrafish, gbx1 and otx2 are among the earliest genes expressed in the neuroectoderm, dividing it into an anterior and a posterior domain with a common border that marks the midbrain–hindbrain boundary (MHB) primordium. Here, we describe the sequence and expression pattern of Gbx1 in mouse. The first transcripts are found at embryonic day 7.75 in the hindbrain. Later on, expression of Gbx1 is detectable in the hindbrain (rhombomeres 2 to 7), spinal cord, optic vesicles, and in the ventral telencephalon. In mouse, Gbx1 expression is not observed at the MHB as is the case during early zebrafish development. We suggest that an evolutionary switch occurred: in mouse Gbx2 is involved in the early specification of the MHB primordium, whereas in zebrafish, gbx1 is required instead of gbx2. Developmental Dynamics 229:334–339, 2004. © 2004 Wiley‐Liss, Inc.
Automatic spoken language identification utilizing acoustic and phonetic speech information

Automatic spoken Language Identi¯cation (LID) is the process of identifying the language spoken within an utterance. The challenge that this task presents is that no prior information is available indicating the content of the utterance or the identity of the speaker. The trend of globalization and the pervasive popularity of the Internet will amplify the need for the capabilities spoken language identi¯ca- tion systems provide. A prominent application arises in call centers dealing with speakers speaking di®erent languages. Another important application is to index or search huge speech data archives and corpora that contain multiple languages. The aim of this research is to develop techniques targeted at producing a fast and more accurate automatic spoken LID system compared to the previous National Institute of Standards and Technology (NIST) Language Recognition Evaluation. Acoustic and phonetic speech information are targeted as the most suitable fea- tures for representing the characteristics of a language. To model the acoustic speech features a Gaussian Mixture Model based approach is employed. Pho- netic speech information is extracted using existing speech recognition technol- ogy. Various techniques to improve LID accuracy are also studied. One approach examined is the employment of Vocal Tract Length Normalization to reduce the speech variation caused by di®erent speakers. A linear data fusion technique is adopted to combine the various aspects of information extracted from speech. As a result of this research, a LID system was implemented and presented for evaluation in the 2003 Language Recognition Evaluation conducted by the NIST.
Simultaneous Fault Isolation and Estimation of Lithium-Ion Batteries via Synthesized Design of Luenberger and Learning Observers

Lithium-ion batteries possess high power, energy, and long cycle life. They are best candidates for applications on hybrid and electric vehicles. To ensure reliable operation, one of the functions in a battery management system is health monitoring in terms of fault diagnosis and estimation. The purpose of this brief is to provide a fault-diagnostic scheme that can achieve single fault isolation and estimation for a three-cell battery string subject to uncertainties. Detecting and isolating faults in systems subject to uncertainties is a challenging task due to the difficulty in distinguishing the effects of faults from uncertainties. To facilitate fault isolation, a bank of systems, each corresponding to a particular fault, are formulated by reorganizing the considered system. Each system in the bank is first transformed into two subsystems. Then, a classical Luenberger observer is designed for the first subsystem to generate a fault-detection residual. In this manner, a bank of reduced-order Luenberger observers are designed to locate a specific fault source, and thus fault isolation is achieved. Parallel to the bank of reduced-order Luenberger observers, a bank of learning observers (LOs) are also constructed to provide an estimate of the isolated fault. As a result, the synthesized design of Luenberger observers and LOs can realize simultaneous fault isolation and estimation. Parameters of an A123 battery cell are extracted via experiments, and effectiveness of the proposed design is demonstrated through simulation studies on the model of a three-cell battery string.
Immunocytochemical localization of GABA, GABAA receptors, and synapse-associated proteins in the developing and adult ferret retina

Abstract Gamma-aminobutyric acid (GABA) modulates the pattern of correlated spontaneous bursting activity between amacrine cells and ganglion cells of the ferret retina during the first postnatal month. Here, we demonstrate the presence of an anatomical network which may underlie these interactions throughout the period when correlated bursting activity is observed, by immunolabelling the neonatal ferret retina for GABA, GABAA receptors, and synapse-associated proteins. GABA immunoreactivity was detected in cell somata in the ganglion cell layer (GCL), in amacrine cells, and in the inner plexiform layer (IPL) by embryonic day 38. This pattern remained largely unchanged throughout neonatal development and in the adult. By contrast to other mammals, the outer plexiform layer (OPL) was only very weakly labelled for GABA, at all ages studied. Strong, punctate, immunolabelling for the β2/3 subunit of the GABAA receptor was apparent in the IPL by birth, and appeared in the OPL by the second postnatal week. The possibility that synaptic interactions in the IPL occur during bursting activity was examined by immunolabelling for synapse-associated proteins. Strong immunoreactivity for synaptic vesicle proteins, Synapsin I and II, and synaptic vesicle-2 (SV2), a synaptic vesicle transporter protein, was observed in the IPL by birth. Immunoreactivity for SNAP-25, a protein associated with vesicle fusion, was also intense at the level of the IPL and in the nerve fiber layer of the retina at birth. Taken together, these patterns of immunoreactivity suggest the presence of a GABAergic network in the IPL of the ferret retina by birth, coinciding with the appearance of correlated bursting activity in the inner retina.
Knockdown of LIM 15 / DMC 1 in the mushroom Coprinus cinereus by double-stranded RNA-mediated gene silencing

Received 20 May 2005 Revised 15 August 2005 Accepted 18 August 2005 The basidiomycete Coprinus cinereus has many advantages as a model organism for studying sexual development and meiosis, but it has been difficult to investigate using reverse-genetics methods, such as gene disruption by homologous recombination. Here, gene repression by dsRNA-mediated gene silencing was tried as an alternative method for reverse-genetics studies. It was shown that transformation of the LIM15/DMC1 dsRNA expression construct (LIM15dsRNA) resulted in genomic insertion of LIM15dsRNA and paucity of the LIM15/DMC1 transcript. First, LIM15dsRNA was transformed into the homothallic strain AmutBmut to generate a homozygote in which both nuclei had a copy of LIM15dsRNA. The LIM15/DMC1-repressed strain showed abnormal homologous chromosome synapsis during meiosis. Basidiospore production was reduced to 16% by the induction of dsRNA. However, approximately 60% of basidiospores were viable. Next, a heterozygote was generated in which one nucleus had a copy of LIM15dsRNA. The phenotype was similar to that of the homozygote. These results are not only the first demonstration of dsRNA-mediated gene silencing in a member of the homobasidiomycete fungi, to which 90% of mushroom species belong, but also the first successful use of a reverse-genetics approach in C. cinereus research.
Development of the hybrid finite element method for applications to heterogeneous materials

In this study, a hybrid finite element method (HFEM) is developed for accurate prediction of the mechanical behavior of heterogeneous materials while maintaining a high level of computational efficiency. A series of physical phenomena arising in heterogeneous materials are investigated using the developed HFEM. These include the analysis of fluid-filled porous materials, thermal expansion mismatch,, microcracking and transformation toughening in heterogeneous materials. To solve these problems, several special elements are constructed based on the Hellinger-Reissner variational principle. Special approximating functions are generated based on Muskhelishvili’s complex variable method. This combination of the finite element method with the analytical approach results in a computationally-efficient method that can easily model the medium with random distribution of inclusions and/or microcracks. In the effort to model the problem of fluid-filled porous material where pores are randomly distributed and each pore is subjected to distinct hydrostatic pressure, a special element with an n-sided pore embedded polygon is constructed. The effect of the pores and hydrostatic pressure applied along the pore surfaces on the local elastic field is well represented in the resulting element formulation. For a thermal expansion mismatch ii problem, the thermo-mechanical coupled problem is first transformed to a purely mechanical problem with prescribed thermal body-force and surface traction acting on the interface between particles and matrix based on the Duhamel-Newmann analogy. Then, a special element with surface traction acting on the interface of particle and matrix is constructed. Residual stress due to thermal expansion mismatch is then obtained by the developed HFEM. To investigate the cracking phenomena in heterogeneous materials, a special crack-tip element with traction acting on the crack surfaces is constructed. For transformation toughening, a special element which can represent the transformation response is constructed. An iterative procedure is presented to investigate the crack growth in the transformation toughening materials. The developed procedure can be applied to the problems of stress-induced transformation toughening to predict the increase of the fracture toughness and transformation zone size for the materials. The proposed method is verified by comparing the results from this study with the traditional FEM simulation results, experimental results, and/or theoretical solutions. From the provided examples, the efficiency of the proposed method can be seen and its accuracy in capturing the local stress distribution along the interface of the inclusions is demonstrated. Such predictions will be very useful towards improving the mechanical behavior of the materials and/or designing of new materials.
Visiting One’s Native Country

The aim of this study was to evaluate to what extent travel-related factors may cause adherence failure to antiretroviral therapy (ART) in otherwise adherent migrants when traveling back to Africa. HIV-infected sub-Saharian migrants living in France with a plasma HIV viral load < 200 copies/mL, with no change in ART for ≥3 months and who were about to visit their native country for between 2 weeks and 6 months were enrolled for the study. Patients completed a self-administered adherence questionnaire both at enrollment and during the week following their return to France. Adherence failure occurred in 23 (11.5%) of 200 patients. Negative perception about ART effectiveness (adjusted odds ratio = 4.3; 95% confidence interval = 1.3-13.7), unexpected traumatic events during their stay in their native country (7.8; 2.3-26.1), and a prolongation of their stay (5.2; 1.4-20.4) were independently associated with a higher likelihood of adherence failure. Owning/renting one’s house in France (0.30; 0.10-0.96), singlehood (0.23; 0.05-1.00), and HIV status disclosure (0.19; 0.05-0.76) were correlates of sustained adherence during traveling.
A stereo echo canceler with correct echo-path identification based on an input-sliding technique

A new stereo echo canceler with correct echo-path identification based on an input-sliding technique is proposed. A time-varying filter located in one of the two channels periodically delays the input signal. By this input sliding, the correct echo-path identification is achieved. Aliasing components and audible clicks by input-sliding are made inaudible by selecting appropriate parameter values for the time-varying filter. Simulations with the NLMS algorithm and a white Gaussian signal confirm the correct echo-path identification. The subjective quality of the input signal with slides is 4.38 based on the ITU-R five-grade impairment scale. Experimental results based on an implementation by 32-bit floating-point digital signal processors show that ERLE is not degraded by talker changes in the remote room. The mean opinion score is as much as 0.55-point higher than the conventional stereo echo canceler for different round-trip delays.
Simple model of collective transport with phase slippage.

On presente une analyse de champ moyen d'un systeme dynamique a plusieurs corps qui modelise le transport de l'onde de densite de charge en presence d'impuretes d'ancrage aleatoires. Le glissement de phase entre les domaines d'onde de densite de charge est modelise pour un terme de couplage qui est periodique dans les differences de phases. Quand il est conduit par un champ externe, le systeme engendre une transition d'ancrage de premier ordre, une hysteresis et une commutation entre les etats d'ancrage et de glissement, et un debut retarde du glissement proche du seuil
NAIST.Japan: Temporal Relation Identification Using Dependency Parsed Tree

In this paper, we attempt to use a sequence labeling model with features from dependency parsed tree for temporal relation identification. In the sequence labeling model, the relations of contextual pairs can be used as features for relation identification of the current pair. Head-modifier relations between pairs of words within one sentence can be also used as the features. In our preliminary experiments, these features are effective for the temporal relation identification tasks.
Analysis of the serine/threonine/tyrosine phosphoproteome of the pathogenic bacterium Listeria monocytogenes reveals phosphorylated proteins related to virulence

Phosphorylation is the most common and widely studied post‐translational protein modification in bacteria. It plays an important role in all kinds of cellular processes and controls key regulatory mechanisms, including virulence in certain pathogens. To gain insight into the role of protein phosphorylation in the pathogen Listeria monocytogenes, the serine (Ser), threonine (Thr) and tyrosine (Tyr) phosphoproteome of this bacterium was determined. We used the “gel free” proteomic approach with high accuracy mass spectrometry after enrichment of phosphopeptides. A total of 143 sites of phosphorylation were clearly identified, on 155 unique peptides of 112 phosphoproteins. The Ser/Thr/Tyr phosphorylation site distribution was 93:43:7. All identified phosphopeptides are monophosphorylated, except one and many identified phosphoproteins are related to virulence, translation, phosphoenolpyruvate:sugar phosphotransferase system, glycolysis and stress response. A description of these phosphoproteins is provided together with a comparison of the phosphosites in the L. monocytogenes proteins and in their homologues of other bacteria for which the phosphoproteome has been determined. Compared with the previous studies, we noticed a more extended conservation of the phosphorylation sites in glycolytic enzymes as well as ribosomal proteins.
UAV-Assisted Heterogeneous Networks for Capacity Enhancement

Modern day wireless networks have tremendously evolved driven by a sharp increase in user demands, continuously requesting more data and services. This puts significant strain on infrastructure-based macro cellular networks due to the inefficiency in handling these traffic demands, cost effectively. A viable solution is the use of unmanned aerial vehicles (UAVs) as intermediate aerial nodes between the macro and small cell tiers for improving coverage and boosting capacity. This letter investigates the problem of user-demand-based UAV assignment over geographical areas subject to high traffic demands. A neural-based cost function approach is formulated, in which UAVs are matched to a particular geographical area. It is shown that leveraging multiple UAVs not only provides long-range connectivity but also better load balancing and traffic offload. Simulation study demonstrates that the proposed approach yields significant improvements in terms of fifth percentile spectral efficiency up to 38% and reduced delays up to 37.5% compared with a ground-based network baseline without UAVs.
CollARt: a tool for creating 3D photo collages using mobile augmented reality

A collage is an artistic composition made by assembling different parts to create a new whole. This procedure can be applied for assembling tridimensional objects. In this paper we present CollARt, a Mobile Augmented Reality application which permits to create 3D photo collages. Virtual pieces are textured with pictures taken with the camera and can be blended with real objects. A preliminary user study (N=12) revealed that participants were able to create interesting works of art. The evaluation also suggested that the possibility of itinerantly mixing virtual pieces with the real world increases creativity.
Multiple Lytic Origins of Replication Are Required for Optimal Gammaherpesvirus Fitness In Vitro and In Vivo

An unresolved question in herpesvirus biology is why some herpesviruses contain more than one lytic origin of replication (oriLyt). Using murine gammaherpesvirus 68 (MHV-68) as model virus containing two oriLyts, we demonstrate that loss of either of the two oriLyts was well tolerated in some situations but not in others both in vitro and in vivo. This was related to the cell type, the organ or the route of inoculation. Depending on the cell type, different cellular proteins, for example Hexim1 and Rbbp4, were found to be associated with oriLyt DNA. Overexpression or downregulation of these proteins differentially affected the growth of mutants lacking either the left or the right oriLyt. Thus, multiple oriLyts are required to ensure optimal fitness in different cell types and tissues.
Indoor Massive MIMO: Uplink Pilot Mitigation Using Channel State Information Map

Massive MIMO brings both motivations and challenges to develop the 5th generation mobile wireless technology. The promising number of users and the high bitrate offered per unit area are challenged by uplink pilot contamination due to pilot reuse and a limited number of orthogonal pilot sequences. This paper proposes a solution to mitigate uplink pilot contamination in an indoor scenario where multi-cell share the same pool of pilot sequences, that are supposed to be less than the number of users. This can be done by reducing uplink pilots using Channel State Information (CSI) prediction. The proposed method is based on machine learning approach, where a quantized version of Channel State Information (QCSI) is learned during estimation session and stored at the Base Station (BS) to be exploited for future CSI prediction. The learned QCSI are represented by a weighted directed graph, which is responsible to monitor and predict the CSI of User Terminals (UTs) in the local cell. We introduce an online learning algorithm to create and update this graph which we call CSI map. Simulation results show an increase in the downlink sum-rate and a significant feedback reduction.
Fine-grained analysis of change couplings

In software evolution analysis, many approaches analyze release history data available through versioning systems. The recent investigations of CVS data have shown that commonly committed files highlight their change couplings. However, CVS stores modifications on the basis of text but does not track structural changes, such as the insertion, removing, or modification of methods or classes. A detailed analysis whether change couplings are caused by source code couplings or by other textual modifications, such as updates in license terms, is not performed by current approaches. The focus of this paper is on adding structural change information to existing release history data. We present an approach that uses the structure compare services shipped with the Eclipse IDE to obtain the corresponding finegrained changes between two subsequent versions of any Java class. This information supports filtering those change couplings which result from structural changes. So we can distill the causes for change couplings along releases and filter out those that are structurally relevant. The first validation of our approach with a medium-sized open source software system showed that a reasonable amount of change couplings are not caused by source code changes.
Generic LSH Families for the Angular Distance Based on Johnson-Lindenstrauss Projections and Feature Hashing LSH

In this paper we propose the creation of generic LSH families for the angular distance based on Johnson-Lindenstrauss projections. We show that feature hashing is a valid J-L projection and propose two new LSH families based on feature hashing. These new LSH families are tested on both synthetic and real datasets with very good results and a considerable performance improvement over other LSH families. While the theoretical analysis is done for the angular distance, these families can also be used in practice for the euclidean distance with excellent results [2]. Our tests using real datasets show that the proposed LSH functions work well for the euclidean distance.