Miracle-dz/UniFAR-FTUs huggingface dataset:
Activation of WNT / β-Catenin Signaling in Pulmonary Fibroblasts by TGF-β1 Is Increased in Chronic Obstructive Pulmonary Disease

Background Chronic obstructive pulmonary disease (COPD) is characterized by abnormal extracellular matrix (ECM) turnover. Recently, activation of the WNT/β-catenin pathway has been associated with abnormal ECM turnover in various chronic diseases. We determined WNT-pathway gene expression in pulmonary fibroblasts of individuals with and without COPD and disentangled the role of β-catenin in fibroblast phenotype and function. Methods We assessed the expression of WNT-pathway genes and the functional role of β-catenin, using MRC-5 human lung fibroblasts and primary pulmonary fibroblasts of individuals with and without COPD. Results Pulmonary fibroblasts expressed mRNA of genes required for WNT signaling. Stimulation of fibroblasts with TGF-β1, a growth factor important in COPD pathogenesis, induced WNT-5B, FZD8, DVL3 and β-catenin mRNA expression. The induction of WNT-5B, FZD6, FZD8 and DVL3 mRNA by TGF-β1 was higher in fibroblasts of individuals with COPD than without COPD, whilst basal expression was similar. Accordingly, TGF-β1 activated β-catenin signaling, as shown by an increase in transcriptionally active and total β-catenin protein expression. Furthermore, TGF-β1 induced the expression of collagen1α1, α-sm-actin and fibronectin, which was attenuated by β-catenin specific siRNA and by pharmacological inhibition of β-catenin, whereas the TGF-β1-induced expression of PAI-1 was not affected. The induction of transcriptionally active β-catenin and subsequent fibronectin deposition induced by TGF-β1 were enhanced in pulmonary fibroblasts from individuals with COPD. Conclusions β-catenin signaling contributes to ECM production by pulmonary fibroblasts and contributes to myofibroblasts differentiation. WNT/β-catenin pathway expression and activation by TGF-β1 is enhanced in pulmonary fibroblasts from individuals with COPD. This suggests an important role of the WNT/β-catenin pathway in regulating fibroblast phenotype and function in COPD.
Synaptic-like Microvesicles of Neuroendocrine Cells Originate from a Novel Compartment That Is Continuous with the Plasma Membrane and Devoid of Transferrin Receptor

We have characterized the compartment from which synaptic-like microvesicles (SLMVs), the neuroendocrine counterpart of neuronal synaptic vesicles, originate. For this purpose we have exploited the previous observation that newly synthesized synaptophysin, a membrane marker of synaptic vesicles and SLMVs, is delivered to the latter organelles via the plasma membrane and an internal compartment. Specifically, synaptophysin was labeled by cell surface biotinylation of unstimulated PC12 cells at 18°C, a condition which blocked the appearance of biotinylated synaptophysin in SLMVs and in which there appeared to be no significant exocytosis of SLMVs. The majority of synaptophysin labeled at 18°C with the membraneimpermeant, cleavable sulfo-NHS-SS–biotin was still accessible to extracellularly added MesNa, a 150-D membrane-impermeant thiol-reducing agent, but not to the 68,000-D protein avidin. The SLMVs generated upon reversal of the temperature to 37°C originated exclusively from the membranes containing the MesNaaccessible rather than the MesNa-protected population of synaptophysin molecules. Biogenesis of SLMVs from MesNa-accessible membranes was also observed after a short (2 min) biotinylation of synaptophysin at 37°C followed by chase. In contrast to synaptophysin, transferrin receptor biotinylated at 18° or 37°C became rapidly inaccessible to MesNa. Immunofluorescence and immunogold electron microscopy of PC12 cells revealed, in addition to the previously described perinuclear endosome in which synaptophysin and transferrin receptor are colocalized, a sub-plasmalemmal tubulocisternal membrane system distinct from caveolin-positive caveolae that contained synaptophysin but little, if any, transferrin receptor. The latter synaptophysin was selectively visualized upon digitonin permeabilization and quantitatively extracted, despite paraformaldehyde fixation, by Triton X-100. Synaptophysin biotinylated at 18°C was present in these subplasmalemmal membranes. We conclude that SLMVs originate from a novel compartment that is connected to the plasma membrane via a narrow membrane continuity and lacks transferrin receptor.
An improved e-mail security protocol

Current e-mail security systems base their security on the secrecy of the long-term private key. If this private key is ever compromised, an attacker can decrypt any messages-past, present or future-encrypted with the corresponding public key. The system described in this paper uses short-term private-key/public-key key pairs to reduce the magnitude of this vulnerability.
Response to Intervention as a Vehicle for Distinguishing Between Children With and Without Reading Disabilities

Children at risk for early reading difficulties were identified on entry into kindergarten, and half of these children received small-group intervention two to three times a week during their kindergarten year. The other half received whatever remedial assistance was offered by their home schools. These children were again assessed at the beginning of first grade, and those who continued to have difficulties in reading received either one-to-one daily tutoring offered by project teachers from the beginning to the end of first grade or whatever remedial assistance was offered by their home schools over the same time period. All target children were periodically assessed through the end of third grade. Results suggest that either kindergarten intervention alone or kindergarten intervention combined with first-grade intervention are both useful vehicles for preventing early and long-term reading difficulties in most at-risk children.
The New Flora of the Volcanic Island of Krakatau

Two hundred years after his birth and 150 years after the publication of ‘On the Origin of Species’, Charles Darwin and his theories are still the focus of worldwide attention. This series offers not only works by Darwin, but also the writings of his mentors in Cambridge and elsewhere, and a survey of the impassioned scientific, philosophical and theological debates sparked by his ‘dangerous idea’.
Crystal structure of (E)-diethyl 2-[(1-phenylsulfonyl-1H-indol-3-yl)methylidene]succinate

In the title compound, C23H23NO6S, the phenyl ring is perpendicular [dihedral angle = 89.34 (9)°] to the indole ring system. In the molecule, the ethoxy groups are each disordered over two sets of sites with occupancy ratios of 0.671 (6):0.329 (6) and 0.75 (3):0.25 (3). The molecular conformation is consolidated by a weak C—H⋯O interaction, which generates an S(6) graph–set motif. The packing of the molecules in the crystal structure features weak C—H⋯π interactions.
Existence and Learning of Teaching Network for CRNN

Existence and Learning of Teaching Network for Complex Recurrent Neural Network (CRNN) has been discussed in this piece of research. Issues related to the quaternionic neural network have been taken into consideration. In this paper by considering the special class of CRNN for which existence of attractive periodic solution in teaching network has been obtained and theoretical results has been proved, limit cycle, existence and uniqueness have also been discussed. This work has very much significant for several real world applications.
Nervous Necrosis Virus Replicates Following the Embryo Development and Dual Infection with Iridovirus at Juvenile Stage in Grouper

Infection of virus (such as nodavirus and iridovirus) and bacteria (such as Vibrio anguillarum) in farmed grouper has been widely reported and caused large economic losses to Taiwanese fish aquaculture industry since 1979. The multiplex assay was used to detect dual viral infection and showed that only nervous necrosis virus (NNV) can be detected till the end of experiments (100% mortality) once it appeared. In addition, iridovirus can be detected in a certain period of rearing. The results of real-time PCR and in situ PCR indicated that NNV, in fact, was not on the surface of the eggs but present in the embryo, which can continue to replicate during the embryo development. The virus may be vertically transmitted by packing into eggs during egg development (formation) or delivering into eggs by sperm during fertilization. The ozone treatment of eggs may fail to remove the virus, so a new strategy to prevent NNV is needed.
Controls on P–T–t deformation path from amphibole zonation during progressive metamorphism of basic rocks (estuary of the River Vilaine, South Brittany, France)

Edenite/tremolite and edenite/magnesio-hornblende in equilibrium with plagioclase, chlorite, epidote, quartz and vapour involve several types of reactions for which KD can be related to T and P. Thermodynamic calculation of these equilibria leads to isopleth systems. Given knowledge of the progressive changes of end-member activities in zoned Ca–Mg amphiboles (based on microprobe analyses), it is possible to construct precise pressure–temperature–time paths (P–T–t paths) which have been followed by metabasites during polyphase metamorphism. When applied to basic rocks from the River Vilaine area, this method allows us to construct a P–T–t path that can be compared directly to the P–T–t path constructed from interbedded acid rocks (aluminous micaschists) in the same structural unit. Through time, both basic and acid rocks underwent the same complex deformation history that can be described conveniently in the L–S fabric system of Flinn. This allows us to construct a P–T–t deformation path for this structural unit. These paths are interpreted in terms of an under/overthrusting continental collision belt (the Hercynian belt), and represent an illustration of the time delay caused by stacking of more than two crustal units.
A comparison among animal models of acute lung injury.

OBJECTIVES To compare four widely used animal models of acute lung injury and to determine the changes in physiologic variables associated with each model. DESIGN A prospective, controlled animal study. SETTING An animal laboratory of a university-affiliated children's hospital. SUBJECTS Four groups of anesthetized, paralyzed, and ventilated young Yorkshire pigs, weighing 35 to 45 kg. INTERVENTIONS Acute lung injury was generated by four different methods: a) intrapulmonary arterial infusion of endotoxin of Escherichia colt; b) bronchoalveolar instillation of 0.05N of hydrochloric acid; c) repeated bronchoalveolar warm saline lavage; and d) intrapulmonary arterial infusion of oleic acid. After each acute lung injury procedure, the temporal changes in various physiologic variables were measured, starting at 60 mins and at 15-min intervals thereafter for a total of 165 mins. Systemic and mixed venous serum immunoreactive tumor necrosis factor (TNF)-alpha concentrations were also measured at the same time points. Analysis of variance for repeated measures was employed to determine the absolute and relative significance of the changes observed. MEASUREMENTS AND MAIN RESULTS Systemic and mixed venous immunoreactive TNF-alpha did not change following any of the acute lung injury procedures. The animals' heart rates and systemic vascular resistances also did not change. Hydrochloric acid instillation as well as bronchoalveolar lavage resulted in significant hypoxemia with no other hemodynamic effects. Endotoxin infusion did not result in hypoxemia but caused significant increases in mean pulmonary arterial pressure and pulmonary vascular resistance and decreases in mean arterial pressure and cardiac output. Oleic acid infusion resulted in a marked hypoxemia with a pronounced increase in mean pulmonary arterial pressure and pulmonary vascular resistance. It also markedly reduced the mean arterial pressure, cardiac output, and the mixed venous PO2. CONCLUSIONS The surfactant depletion and hydrochloric acid instillation models produce acute hypoxemia in an otherwise hemodynamically stable animal. A brief endotoxin infusion provides a model for cardiovascular instability and pulmonary hypertension but fails to produce hypoxemia in the pig. The oleic acid infusion creates a model of marked cardiovascular instability, pulmonary hypertension, and profound hypoxemia. However, none of the acute lung injury models described was associated with the production of tumor necrosis factor.
Radiometric calibration of spacecraft using small lunar images

The Moon is the only object that is accessible to Earth- orbiting imaging systems, whose brightness is within the dynamic range of most such systems, and whose spectral radiance is potentially knowable to a fraction of a percent. As such, it is a desirable target for radiometric calibration. Several spacecraft teams have begun using or are planning to use lunar observations as part of their calibration process. We examine the data reduction steps that can be used to extract the lunar irradiance from low resolution images of the Moon and qualitatively assess the attendant uncertainties. Images of the Moon provide a precise measure of scattered- light sensitivity. The response integrated over an image is compared to a lunar irradiance model being developed from terrestrial multi-band photometric observations over the 350 - 2500 nm range. For SeaWiFS images, wherein the Moon is about 6 by 20 pixels, the uncertainty in extracting the total lunar signal from the image is about 1% for most bands. A significant source of uncertainty is knowledge of the spacecraft inertial pitch rate, which is currently derived form image analysis. The very low noise in some of the detectors limits knowledge of the zero radiance level to 1/2 of a Data Number. A program is underway to accurately determine at several wavelengths the brightness variations of the Moon associated with Sun-Moon-observer Geometry. Comparisons with Earth-based lunar radiometric observations for relative responsivity (changes of spacecraft instrument gain with time) are consistent to about 1/2 the formal uncertainty. At present, the largest errors in using these data for absolute radiometric calibration are in the lunar radiance model.
A freeway traffic control model by first order hybrid Petri nets

The paper proposes a model for real time control of freeways by ramp metering, an emerging technique for efficient freeway management. A modular framework based on first order hybrid Petri nets models the vehicle flows by a first order fluid approximation. Moreover, the lane interruptions and the signal timing plan controlling on-ramps are described by the discrete event dynamics using timed Petri nets. The proposed formalism enables the network designer to choose suitable ramp metering control signals in order to maximize the traffic flow by optimizing a suitable objective function. The optimal mode of operation is performed based on the state knowledge of the obtained linear discrete-time, time-varying state variable model of the freeway to react to unpredictable events such as the blocking of a lane due to an accident or to work in progress. The proposed model is applied to a case study to show its effectiveness.
Turbulence Characteristics of Sediment‐Laden Flows in Open Channels

The turbulence characteristics of sediment‐laden flows in open channels are investigated using two‐component laser‐Doppler velocimetry. Suspensions of well‐sorted sands with diameters ranging from 0.15 mm to 0.24 mm, flowing over nominally flat beds, both fixed and erodible, are studied in a tiltable, recirculating flume. Various conceptual models that have been proposed to explain the mean‐field profiles are examined for consistency with respect to their implications for higher‐order characteristics. No evidence is found to support either the traditional model, associated with a decrease in the von Karman constant, or the more recently proposed models based on simple analogies to slightly stably stratified wall‐bounded flows. A model based on small‐scale fluid‐particle interaction is suggested as more promising.
Microsimulating Weekend Travel by Households in Calgary

A tour-based microsimulation of household weekend travel behavior is being developed that uses data collected from the roughly 1,400 households who were assigned a weekend survey day in a household activity survey conducted in the Calgary Region in 2001. This paper describes the work being done, including the design of the system, the estimation process for the choice models used to establish the sampling distributions for the Monte Carlo processes used to assign states (simulating choices made) at various points in the microsimulation, and the calibration of the resulting system consistent with available aggregate targets.
Generation of fundamental frequency contours of Mandarin in HMM-based speech synthesis using generation process model

The HMM-based speech synthesis system can produce high quality synthetic speech with flexible modeling of spectral and prosodic parameters. In this approach, short term spectra, fundamental frequency (F0) and duration are generated by multi-stream HMMs separately. However the quality of synthetic speech degrades when feature vectors used in training are noisy. Among all noisy features, pitch tracking errors and corresponding flawed voiced/unvoiced (VU) decisions are the two key factors in voice quality problems. Pitch tracking errors occur more often in Mandarin vowels of Tone 3 and Tone 4, because the pitch of these vowels can be very low and sometimes treated as aperiodic signal. On the other hand, F0 values in unvoiced regions, such as consonants, are normally defined as unavailable; it is then impossible to use standard HMMs for F0 modeling. Currently a preferred method to solve this is to use a multi-space distribution HMM (MSDHMM). In this approach, discrete distributions are used for modeling the VU decision and continuous Gaussian distributions are used for F0 modeling within the voiced regions. Due to this assumption of undefined F0 values in unvoiced regions and the special structure of MSDHMM, the generated F0 values are limited in accuracy. In this paper, an F0 generation process model is used to estimate F0 values in the region of pitch tracking errors, as well as in unvoiced regions. A prior knowledge of VU is imposed in each Mandarin phoneme and then used for VU decision. Thus the F0 can be modeled within the standard HMM framework.
Dispersion and nonlinear effects in the 2011 Tohoku‐Oki earthquake tsunami

This study reveals the roles of the wave dispersion and nonlinear effects for the 2011 Tohoku-Oki earthquake tsunami. We conducted tsunami simulations based on the nonlinear dispersive equations with a high-resolution source model. The simulations successfully reproduced the waveforms recorded in the offshore, deep sea, and focal areas. The calculated inundation area coincided well with the actual inundation for the Sendai Plain, which was the widest inundation area during this event. By conducting sets of simulations with different tsunami equations, we obtained the followings insights into the wave dispersion, nonlinear effects, and energy dissipation for this event. Although the wave dispersion was neglected in most studies, the maximum amplitude was significantly overestimated in the deep sea if the dispersion was not included. The waveform observed at the station with the largest tsunami height (∼2 m) among the deep-ocean stations also verified the necessity of the dispersion. It is well known that the nonlinear effects play an important role for the propagation of a tsunami into bays and harbors. Additionally, nonlinear effects need to be considered to accurately model later waves, even for offshore stations. In particular, including nonlinear terms rather than the inundation was more important when precisely modeling the waves reflected from the coast.
Learning the Bayesian Network Structure: Dirichlet Prior versus Data

In the Bayesian approach to structure learning of graphical models, the equivalent sample size (ESS) in the Dirichlet prior over the model parameters was recently shown to have an important effect on the maximum-a-posteriori estimate of the Bayesian network structure. In our first contribution, we theoretically analyze the case of large ESS-values, which complements previous work: among other results, we find that the presence of an edge in a Bayesian network is favoured over its absence even if both the Dirichlet prior and the data imply independence, as long as the conditional empirical distribution is notably different from uniform. In our second contribution, we focus on realistic ESS-values, and provide an analytical approximation to the "optimal" ESS-value in a predictive sense (its accuracy is also validated experimentally): this approximation provides an understanding as to which properties of the data have the main effect determining the "optimal" ESS-value.
Orthogonalized Spatial Multiplexing for Closed-Loop MIMO Systems

In this paper, we propose a novel spatial multiplexing (SM) scheme for transmission over flat-fading multiple-input multiple-output (MIMO) channels, which allows simple maximum-likelihood decoding at the receiver with small feedback information. We begin with a real-valued representation of the complex-valued system model, and show that we can achieve orthogonality between transmitted signals by applying a proper rotation to transmitted symbols. Compared with other closed-loop methods, the proposed scheme significantly reduces the processing complexity at both transmitter and receiver as well as the feedback overhead. We also combine the proposed orthogonalization method with antenna-selection techniques, and then discuss a criterion based on the minimum Euclidean distance between received vectors for selecting the optimal subset of multiple transmit antennas. Using geometrical properties of the receive constellations, we also present a simple antenna-selection metric for the proposed SM systems. Simulation results demonstrate that our SM system performs close to the optimum closed-loop system with much-reduced complexity
Anti-biotin Antibodies Offer Superior Organelle-specific Labeling of Mitochondria over Avidin or Streptavidin

The mitochondrial matrix contains endogenously biotinylated proteins. These proteins can cause unexpected background signal when biotin–avidin- or biotin–streptavidin-based detection systems are used in immunocytochemistry. Here we show that this reactivity can be deliberately exploited, using a simple anti-biotin reagent, to obtain strong and highly specific labeling of mitochondria by both light and electron microscopy. The signal is substantially stronger than when either avidin or streptavidin is used to detect the endogenous biotin. These results confirm the accessibility of protein-bound endogenous biotin to exogenous probes, and localize the biotinylated enzymes to the mitochondrial matrix. (J Histochem Cytochem 45:1053–1057, 1997)