Miracle-dz/UniFAR-FTUs huggingface dataset:
The circular definition of populations and its implications for biological sampling

Application of population‐based theoretical models to the study of real world populations requires the relationship between the real and theoretical populations to be defined. Otherwise, it is not possible to take a representative field sample or census of a population. I demonstrate that the concept of a biological population is based on a circular definition and is logically untenable. A population is composed of a number of individuals whose membership of the population is determined by their relationship to the rest of the population. This has serious implications for common practice in a range of ecological and evolutionary disciplines.
Non-Photochemical Quenching Capacity in Arabidopsis thaliana Affects Herbivore Behaviour

Under natural conditions, plants have to cope with numerous stresses, including light-stress and herbivory. This raises intriguing questions regarding possible trade-offs between stress defences and growth. As part of a program designed to address these questions we have compared herbivory defences and damage in wild type Arabidopsis thaliana and two “photoprotection genotypes”, npq4 and oePsbS, which respectively lack and overexpress PsbS (a protein that plays a key role in qE-type non-photochemical quenching). In dual-choice feeding experiments both a specialist (Plutella xylostella) and a generalist (Spodoptera littoralis) insect herbivore preferred plants that expressed PsbS most strongly. In contrast, although both herbivores survived equally well on each of the genotypes, for oviposition female P. xylostella adults preferred plants that expressed PsbS least strongly. However, there were no significant differences between the genotypes in levels of the 10 most prominent glucosinolates; key substances in the Arabidopsis anti-herbivore chemical defence arsenal. After transfer from a growth chamber to the field we detected significant differences in the genotypes’ metabolomic profiles at all tested time points, using GC-MS, but no consistent “metabolic signature” for the lack of PsbS. These findings suggest that the observed differences in herbivore preferences were due to differences in the primary metabolism of the plants rather than their contents of typical “defence compounds”. A potentially significant factor is that superoxide accumulated most rapidly and to the highest levels under high light conditions in npq4 mutants. This could trigger changes in planta that are sensed by herbivores either directly or indirectly, following its dismutation to H2O2.
Using the Optical Mouse Sensor as a Two-Euro Counterfeit Coin Detector

In this paper, the sensor of an optical mouse is presented as a counterfeit coin detector applied to the two-Euro case. The detection process is based on the short distance image acquisition capabilities of the optical mouse sensor where partial images of the coin under analysis are compared with some partial reference coin images for matching. Results show that, using only the vision sense, the counterfeit acceptance and rejection rates are very similar to those of a trained user and better than those of an untrained user.
Robust lower bounds for communication and stream computation

We study the communication complexity of evaluating functions when the input data is randomly allocated (according to some known distribution) amongst two or more players, possibly with information overlap. This naturally extends previously studied variable partition models such as the best-case and worst-case partition models [32,29]. We aim to understand whether the hardness of a communication problem holds for almost every allocation of the input, as opposed to holding for perhaps just a few atypical partitions. A key application is to the heavily studied data stream model. There is a strong connection between our communication lower bounds and lower bounds in the data stream model that are "robust" to the ordering of the data. That is, we prove lower bounds for when the order of the items in the stream is chosen not adversarially but rather uniformly (or near-uniformly) from the set of all permuations. This random-order data stream model has attracted recent interest, since lower bounds here give stronger evidence for the inherent hardness of streaming problems. Our results include the first random-partition communication lower bounds for problems including multi-party set disjointness and gap-Hamming-distance. Both are tight. We also extend and improve previous results [19,7] for a form of pointer jumping that is relevant to the problem of selection (in particular, median finding). Collectively, these results yield lower bounds for a variety of problems in the random-order data stream model, including estimating the number of distinct elements, approximating frequency moments, and quantile estimation.
Enhancement of Rossby Wave Breaking by Steep Potential Vorticity Gradients in the Winter Stratosphere

This work investigates the extent to which potential vorticity gradients affect the vertical propagation of planetary-scale Rossby waves on the edge of a stratospheric polar vortex and their eventual nonlinear saturation and breaking. Using two different numerical modeling approaches, it is shown that wave propagation and wave breaking are significantly reduced when the potential vorticity gradients at the vortex edge are anomalously weak. The efficiency of the first model, based on high-resolution contour dynamics, permits a full exploration of the parameter space of wave forcing amplitude and edge steepness. A more realistic primitive equation model in spherical geometry both confirms the contour dynamics results and highlights some direct implications for stratospheric modeling in more comprehensive models. The results suggest that stratospheric models using horizontal resolutions of spectral T42 or less may significantly underestimate the vertical propagation and breaking of planetary waves, and may consequently misrepresent such important stratospheric processes as the mean meridional circulation, sudden warmings, and the mixing of chemically distinct polar and midlatitude air.
Machine Learning Algorithms for Opinion Mining and Sentiment Classification

With the evolution of web technology, there is a huge amount of data present in the web for the internet users. These users not only use the available resources in the web, but also give their feedback, thus generating additional useful information. Due to overwhelming amount of user's opinions, views, feedback and suggestions available through the web resources, it's very much essential to explore, analyse and organize their views for better decision making. Opinion Mining or Sentiment Analysis is a Natural Language Processing and Information Extraction task that identifies the user's views or opinions explained in the form of positive, negative or neutral comments and quotes underlying the text. Various supervised or data-driven techniques to Sentiment analysis like Naive Byes, Maximum Entropy and SVM.For classification use support vector machine (SVM), it performs the sentiment classification task also consider sentiment classification accuracy.
The Pim-1 Protein Kinase Is an Important Regulator of MET Receptor Tyrosine Kinase Levels and Signaling

ABSTRACT MET, the receptor for hepatocyte growth factor (HGF), plays an important role in signaling normal and tumor cell migration and invasion. Here, we describe a previously unrecognized mechanism that promotes MET expression in multiple tumor cell types. The levels of the Pim-1 protein kinase show a positive correlation with the levels of MET protein in human tumor cell lines and patient-derived tumor materials. Using small interfering RNA (siRNA), Pim knockout mice, small-molecule inhibitors, and overexpression of Pim-1, we confirmed this correlation and found that Pim-1 kinase activity regulates HGF-induced tumor cell migration, invasion, and cell scattering. The novel biochemical mechanism for these effects involves the ability of Pim-1 to control the translation of MET by regulating the phosphorylation of eukaryotic initiation factor 4B (eIF4B) on S406. This targeted phosphorylation is required for the binding of eIF4B to the eIF3 translation initiation complex. Importantly, Pim-1 action was validated by the evaluation of patient blood and bone marrow from a phase I clinical trial of a Pim kinase inhibitor, AZD1208. These results suggest that Pim inhibitors may have an important role in the treatment of patients where MET is driving tumor biology.
Enhanced intelligent driver model to access the impact of driving strategies on traffic capacity

With an increasing number of vehicles equipped with adaptive cruise control (ACC), the impact of such vehicles on the collective dynamics of traffic flow becomes relevant. By means of simulation, we investigate the influence of variable percentages of ACC vehicles on traffic flow characteristics. For simulating the ACC vehicles, we propose a new car-following model that also serves as the basis of an ACC implementation in real cars. The model is based on the intelligent driver model (IDM) and inherits its intuitive behavioural parameters: desired velocity, acceleration, comfortable deceleration and desired minimum time headway. It eliminates, however, the sometimes unrealistic behaviour of the IDM in cut-in situations with ensuing small gaps that regularly are caused by lane changes of other vehicles in dense or congested traffic. We simulate the influence of different ACC strategies on the maximum capacity before breakdown and the (dynamic) bottleneck capacity after breakdown. With a suitable strategy, we find sensitivities of the order of 0.3, i.e. 1 per cent more ACC vehicles will lead to an increase in the capacities by about 0.3 per cent. This sensitivity multiplies when considering travel times at actual breakdowns.
Analysis and observation of polarimetric scattering behavior in wetland area

This paper proposes a simple monitoring technique for water area change in wetland environment based on POLSAR image analysis. From the results of the image analysis by utilizing fully or quad. polarimetric SAR data set, it is found that strong double-bounce scattering can be observed at the vicinity of the boundary region between water area and the surrounding emerged-plants area. This peculiar scattering feature is utilized as a useful marker for estimating the water area change. To verify the generating mechanism of the double-bounce scattering, the Finite-Difference TimeDomain (FDTD) polarimetric scattering analysis is also carried out for a simplified water-emergent boundary model. The dependency of the polarimetric scattering feature on the variation of the radar incident angle, the change of the biomass and material parameters of the surrounding emerged-plants is investigated. Resultantly, it is confirmed from the detailed FDTD analysis that by using the proposed technique, one can estimate the true water area change in wetland and its surrounding area in all seasons.
Power delay tradeoff for dynamic data compression and transmission over a wireless channel

We consider an average delay minimization problem for a power limited transmitter which collects and compresses correlated bits from multiple sources for transmission to a sink over a fading wireless channel. We propose a compression and transmission policy that trades off the average total power in compression and transmission with the average delay of bits. We present analytical bounds and simulation results showing that the tradeoff performance of our policy is better than for a previously known policy in a power limited regime.
Cytotoxic Mechanism of Selenomethionine in Yeast*

Background: Selenomethionine cytotoxicity has not been completely elucidated even though it is often used for phase determination in X-ray crystallography. Results: Yeast strain genetically modified to increase intracellular thiol compounds showed selenomethionine resistance. Conclusion: Selenomethionine induces depletion of intracellular thiol compounds in yeast cells. Significance: This work is the first report of cytotoxicity mechanism of selenomethionine in view point of its metabolite. Although selenium is an essential element, its excessive uptake is detrimental to living organisms. The significance of selenium for living organisms has been exploited for various purposes. However, the molecular basis of selenium toxicity is not completely understood. Here, we applied a capillary electrophoresis time-of-flight mass spectrometry-based metabolomics approach to analysis of yeast cells treated with selenomethionine. The data indicated that intracellular thiol compounds are significantly decreased, and diselenide and selenosulfide compounds are increased in selenomethionine-treated cells. The growth defect induced by selenomethionine was recovered by extracellular addition of cysteine and by genetic modification of yeast cells that have an additional de novo synthetic pathway for cysteine. Because cysteine is an intermediate of thiol compounds, these results suggested that the loss of a reduced form of thiol compounds due to selenomethionine causes a growth defect of yeast cells.
AZD1480 Blocks Growth and Tumorigenesis of RET- Activated Thyroid Cancer Cell Lines

Persistent RET activation is a frequent event in papillary thyroid carcinoma (PTC) and medullary thyroid carcinoma (MTC). In these cancers, RET activates the ERK/MAPK, the PI3K/AKT/mTOR and the JAK/STAT3 pathways. Here, we tested the efficacy of a JAK1/2- inhibitor, AZD1480, in the in vitro and in vivo growth of thyroid cancer cell lines expressing oncogenic RET. Thyroid cancer cell lines harboring RET/PTC1 (TPC-1), RET M918T (MZ-CRC1) and RET C634W (TT) alterations, as well as TPC-1 xenografts, were treated with JAK inhibitor, AZD1480. This inhibitor led to growth inhibition and/or apoptosis of the thyroid cancer cell lines in vitro, as well as to tumor regression of TPC-1 xenografts, where it efficiently blocked STAT3 activation in tumor and stromal cells. This inhibition was associated with decreased proliferation, decreased blood vessel density, coupled with increased necrosis. However, AZD1480 repressed the growth of STAT3- deficient TPC-1 cells in vitro and in vivo, demonstrating that its effects in this cell line were independent of STAT3 in the tumor cells. In all cell lines, the JAK inhibitor reduced phospho-Y1062 RET levels, and mTOR effector phospho-S6, while JAK1/2 downregulation by siRNA did not affect cell growth nor RET and S6 activation. In conclusion, AZD1480 effectively blocks proliferation and tumor growth of activated RET- thyroid cancer cell lines, likely through direct RET inhibition in cancer cells as well as by modulation of the microenvironment (e.g. via JAK/phospho-STAT3 inhibition in endothelial cells). Thus, AZD1480 should be considered as a therapeutic agent for the treatment of RET- activated thyroid cancers.
Interleukin 18 gene polymorphisms predict risk and outcome of Alzheimer’s disease

Background and aim: Inflammation has been extensively implicated in the pathogenesis of Alzheimer’s disease (AD). Although there is evidence of a key role for cytokines in neuroinflammation processes, so far the proinflammatory cytokine interleukin (IL)-18 has not been associated with AD. The aim of this study was to investigate the impact of two polymorphisms of the human IL-18 gene promoter at positions −607 (C/A) and −137 (G/C) on both susceptibility to and progression of AD. Results: The results revealed that the genotype distribution of the −607 (C/A) polymorphism was different between patients with AD and control subjects (χ2 = 7.99, df = 2, p = 0.0184). In particular, carriers of the CC genotype were at increased risk of developing AD (OR 2.33; 95% CI 1.29 to 4.22; p = 0.0052). The observed genotypes were in Hardy–Weinberg equilibrium, as for the −607 polymorphism, whereas the −137 polymorphism appeared in Hardy–Weinberg disequilibrium only in the patient group (p = 0.0061). Finally, in a 2 year follow-up study, the −137 CC genotype was strongly and specifically associated with a faster cognitive decline (F = 4.024; df = 4,192; p = 0.0037 for time by IL-18 −137 G/C group interaction) with no interaction effect with the apolipoprotein E ε4/non-ε4 allele presence. Conclusion: As IL-18 cytokine promoter gene polymorphisms have been previously described to have functional consequences on IL-18 expression, it is possible that individuals with a prevalent IL-18 gene variant have a dysregulated immune response, suggesting that IL-18 mediated immune mechanisms may play a crucial role in AD.
Asymptotic capacity and optimal precoding strategy of multi-level precode & forward in correlated channels

We analyze a multi-level MIMO relaying system where a multiple-antenna transmitter sends data to a multiple-antenna receiver through several relay levels, also equipped with multiple antennas. Assuming correlated fading in each hop, each relay receives a faded version of the signal transmitted by the previous level, performs precoding on the received signal and retransmits it to the next level. Using free probability theory and assuming that the noise power at the relay levels - but not at the receiver - is negligible, a closed-form expression of the end-to-end asymptotic instantaneous mutual information is derived as the number of antennas in all levels grow large with the same rate. This asymptotic expression is shown to be independent from the channel realizations, to only depend on the channel statistics and to also serve as the asymptotic value of the end-to-end average mutual information. We also provide the optimal singular vectors of the precoding matrices that maximize the asymptotic mutual information : the optimal transmit directions represented by the singular vectors of the precoding matrices are aligned on the eigenvectors of the channel correlation matrices, therefore they can be determined only using the known statistics of the channel matrices and do not depend on a particular channel realization.
Growth Hormone Determines Sexual Dimorphism of Hepatic Cytochrome P450 3A4 Expression in Transgenic Mice

The impact of age and sex on the expression of hepatic cytochrome P450 3A4 (CYP3A4) was recently determined in a transgenic mouse line carrying the human CYP3A4 gene. To further investigate the physiological regulation of human CYP3A genes, a novel transgenic mouse line was generated using a bacterial artificial chromosome clone containing both CYP3A4 and CYP3A7 genes. CYP3A7 expression was observed in transgenic mouse fetal livers, whereas CYP3A4 exhibited developmental expression characterized by sexual dimorphism in postpubertal livers. Hepatic CYP3A4 protein and RNA were expressed in immature transgenic male mice and became undetectable after 6 weeks of age, whereas CYP3A4 was expressed in both immature and adult females. CYP3A4 was markedly elevated by the xenobiotic receptor activator phenobarbital in both male and female livers, demonstrating drug induction of the CYP3A4 transgene in this mouse model. Furthermore, continuous infusion of recombinant growth hormone (GH) in transgenic male mice, overriding the pulsatile male plasma GH profile, increased hepatic CYP3A4 mRNA and protein to normal female levels. Continuous GH treatment also feminized the expression of endogenous murine Cyp2b and Cyp3a44 genes. Thus, human CYP3A4 contains all of the gene regulatory sequences required for it to respond to endogenous hormonal regulators of developmental expression and sexual dimorphism, in particular GH. These findings may help elucidate the role of GH in determining the sex-dependent expression of CYP3A4 in human liver and suggest that GH therapy may alter the pharmacokinetic and pharmacodynamic properties of CYP3A4 substrates, leading to enhanced metabolism and disposition of drugs in men.
Dynamics of Trigger Factor Interaction with Translating Ribosomes*

In all organisms ribosome-associated chaperones assist early steps of protein folding. To elucidate the mechanism of their action, we determined the kinetics of individual steps of the ribosome binding/release cycle of bacterial trigger factor (TF), using fluorescently labeled chaperone and ribosome-nascent chain complexes. Both the association and dissociation rates of TF-ribosome complexes are modulated by nascent chains, whereby their length, sequence, and folding status are influencing parameters. However, the effect of the folding status is modest, indicating that TF can bind small globular domains and accommodate them within its substrate binding cavity. In general, the presence of a nascent chain causes an up to 9-fold increase in the rate of TF association, which provides a kinetic explanation for the observed ability of TF to efficiently compete with other cytosolic chaperones for binding to nascent chains. Furthermore, a subset of longer nascent polypeptides promotes the stabilization of TF-ribosome complexes, which increases the half-life of these complexes from 15 to 50 s. Nascent chains thus regulate their folding environment generated by ribosome-associated chaperones.
Preamble-Based Channel Estimation for Amplify-and-Forward OFDM Relay Networks

In this paper, we address the preamble-based channel estimation problem for orthogonal frequency-division multiplexing (OFDM) systems using multiple amplify-and-forward (AF) relays. We first establish a linear minimum mean-square-error (LMMSE) channel estimator which directly estimates the overall channels from the source to the destination. Then, based on the assumption that the channel correlations between the relays are unknown at the source terminal, a suboptimal training sequence and precoding matrices in closed form are designed to approach the optimal estimation performance at low-complexity.
Event detection in tennis matches based on video data mining

This paper proposes a mining-based method to achieve event detection for broadcasting tennis videos. Utilizing visual and aural information, we extract some high-level features to describe video segments. The audiovisual features are further transformed to symbolic streams and an efficient mining technique is applied to derive all frequent patterns that characterize tennis events. After mining, we categorize frequent patterns into several kinds of events and therefore achieve event detection for tennis videos by checking the correspondence between mined patterns and events. The experimental results show that the proposed approach is a promising way to detect events in broadcasting tennis video.