Miracle-dz/UniFAR-FTUs huggingface dataset:
Physical, metabolic and developmental functions of the seed coat

The conventional understanding of the role of the seed coat is that it provides a protective layer for the developing zygote. Recent data show that the picture is more nuanced. The seed coat certainly represents a first line of defense against adverse external factors, but it also acts as channel for transmitting environmental cues to the interior of the seed. The latter function primes the seed to adjust its metabolism in response to changes in its external environment. The purpose of this review is to provide the reader with a comprehensive view of the structure and functionality of the seed coat, and to expose its hidden interaction with both the endosperm and embryo. Any breeding and/or biotechnology intervention seeking to increase seed size or modify seed features will have to consider the implications on this tripartite interaction.
High-level feature representation using recurrent neural network for speech emotion recognition

This paper presents a speech emotion recognition system using a recurrent neural network (RNN) model trained by an efficient learning algorithm. The proposed system takes into account the long-range context effect and the uncertainty of emotional label expressions. To extract high-level representation of emotional states with regard to its temporal dynamics, a powerful learning method with a bidirectional long short-term memory (BLSTM) model is adopted. To overcome the uncertainty of emotional labels, such that all frames in the same utterance are mapped into the same emotional label, it is assumed that the label of each frame is regarded as a sequence of random variables. Then, the sequences are trained by the proposed learning algorithm. The weighted accuracy of the proposed emotion recognition system is improved up to 12% compared to the DNN-ELM based emotion recognition system used as a baseline.
The icing on the cake - combining relational and semantic methods to extract meaning from online message board postings

In recent years, we have seen a rapid growth of online communities on the Web. These virtual communities serve as socio-technical platforms for various professionals, entrepreneurs and serious hobbyists to engage in discussion around a shared area of interest. They mostly use these platforms to exchange knowledge and expertise. So far, online communities have been analysed either via the structure of the communities or the content of messages and the motivations of members. We argue that in order to gain insight in the dynamics of online communities, we have to combine a set of methods that allows for the analysis of both the structure as well as the content of communications in these communities. Empirical studies in the domain of online communities usually employ a single method. Often, motivations to participate in these communities were investigated [e.g., 1, 2]. Other research focused on behaviour of community members [e.g., 3, 4]. Some of these studies employed qualitative methods, especially case studies [5-6] and ethnographies [7-8]. However, studies that combine different methods are scarce [9]. This holds in particular for studies that focus on relational (using social network analysis) and interpretational information (using for example semantic maps). To our knowledge, studies that employ both methods are lacking. With this paper, we want to contribute to the literature by proposing a way to combine both approaches. We illustrate the approach with data from an online community, and discuss implications for researchers.
Nup2p Dynamically Associates with the Distal Regions of the Yeast Nuclear Pore Complex

Nucleocytoplasmic transport is mediated by the interplay between soluble transport factors and nucleoporins resident within the nuclear pore complex (NPC). Understanding this process demands knowledge of components of both the soluble and stationary phases and the interface between them. Here, we provide evidence that Nup2p, previously considered to be a typical yeast nucleoporin that binds import- and export-bound karyopherins, dynamically associates with the NPC in a Ran-facilitated manner. When bound to the NPC, Nup2p associates with regions corresponding to the nuclear basket and cytoplasmic fibrils. On the nucleoplasmic face, where the Ran–GTP levels are predicted to be high, Nup2p binds to Nup60p. Deletion of NUP60 renders Nup2p nucleoplasmic and compromises Nup2p-mediated recycling of Kap60p/Srp1p. Depletion of Ran–GTP by metabolic poisoning, disruption of the Ran cycle, or in vitro by cell lysis, results in a shift of Nup2p from the nucleoplasm to the cytoplasmic face of the NPC. This mobility of Nup2p was also detected using heterokaryons where, unlike nucleoporins, Nup2p was observed to move from one nucleus to the other. Together, our data support a model in which Nup2p movement facilitates the transition between the import and export phases of nucleocytoplasmic transport.
Tumorigenicity and metabolism of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol enantiomers and metabolites in the A/J mouse.

4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL), a major metabolite of the tobacco-specific pulmonary carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), has a chiral center but the tumorigenicity of the NNAL enantiomers has not been previously examined. In this study, we assessed the relative tumorigenic activities in the A/J mouse of NNK, racemic NNAL, (R)-NNAL, (S)-NNAL and several NNAL metabolites, including [4-(methylnitrosamino)-1-(3-pyridyl)but-(S)-1-yl] beta-O-D-gluco-siduronic acid [(S)-NNAL-Gluc], 4-(methylnitrosamino)-1-(3-pyridyl N-oxide)-1-butanol, 5-(3-pyridyl)-2-hydroxytetrahydrofuran, 4-(3-pyridyl)butane-1,4-diol and 2-(3-pyridyl) tetrahydrofuran. We also quantified urinary metabolites of racemic NNAL and its enantiomers and investigated their metabolism with A/J mouse liver and lung microsomes. Groups of female A/J mice were given a single i.p. injection of 20 micromol of each compound and killed 16 weeks later. Based on lung tumor multiplicity, (R)-NNAL (25.6 +/- 7.5 lung tumors/mouse) was as tumorigenic as NNK (25.3 +/- 9.8) and significantly more tumorigenic than racemic NNAL (12.1 +/- 5.6) or (S)-NNAL (8.2 +/- 3.3) (P < 0. 0001). None of the NNAL metabolites was tumorigenic. The major urinary metabolites of racemic NNAL and the NNAL enantiomers were 4-hydroxy-4-(3-pyridyl)butanoic acid (hydroxy acid), NNAL-N-oxide and NNAL-Gluc, in addition to unchanged NNAL. Treatment with (R)-NNAL or (S)-NNAL gave predominantly (R)-hydroxy acid or (S)-hydroxy acid, respectively, as urinary metabolites. While treatment of mice with racemic or (S)-NNAL resulted in urinary excretion of (S)-NNAL-Gluc, treatment with (R)-NNAL gave both (R)-NNAL-Gluc and (S)-NNAL-Gluc in urine, apparently through the metabolic intermediacy of NNK. (S)-NNAL appeared to be a better substrate for glucuronidation than (R)-NNAL in the A/J mouse. Mouse liver and lung microsomes converted NNAL to products of alpha-hydroxylation, to NNAL-N-oxide, to adenosine dinucleotide phosphate adducts and to NNK. In lung microsomes, metabolic activation by alpha-hydroxylation of (R)-NNAL was significantly greater than that of (S)-NNAL. The results of this study provide a metabolic basis for the higher tumorigenicity of (R)-NNAL than (S)-NNAL in A/J mouse lung, namely preferential metabolic activation of (R)-NNAL in lung and preferential glucuronidation of (S)-NNAL.
Virtual Integration of Cyber-Physical Systems by Verification

In this position paper, we advocate the use of verification technology to tackle the virtual integration problem for cyber-physical systems. In particular, we advocate the use of high-level modeling languages that allow designers to declaratively specify what properties their architectural models should have, not how to achieve them. We further advocate the use of verification technology to analyze such models, in particular to synthesize concrete architectural models that certifiably satisfy all properties. We discuss our work in this direction and outline some of the challenges. Specifically, we show that virtual integration in the presence of real-time scheduling constraints leads to problems that cannot be dealt with in a compositional manner. They can, however, be handled in a semi-compositional fashion, as we outline in this paper.
Avoiding vote loss by changing policy positions

This paper addresses the electoral consequences of the German government’s anti-nuclear power policy shift after the Fukushima accident. Building on a cost-benefit framework and insights from political psychology, the theoretical analysis anticipates that the policy shift could not earn governing parties additional votes but could avoid vote loss. Utilizing data from multiple surveys and employing simulation techniques, the evidence demonstrates that voters, in particular incumbents’ supporters, became more skeptical of nuclear power after the Fukushima disaster. At the same time, governing parties’ supporters were particularly eager to perceive a credible change in the government’s nuclear power stance. As a consequence, governing parties did not garner additional votes but inhibited their supporters from voting for other parties and thus avoided vote loss. Generally speaking, the novel approach proposed in this paper is suitable for shedding light on electoral effects of parties’ policy shifts that have thus far gone unnoticed.
Independent versus repeated measurements: A performance quantification via state evolution

The paper quantifies and compares the exact asymptotic performance of multiple measurement vector (MMV) and distributed sensing (DS) models. Both models assume multiple measurement instances yk = Akxk + wk, k = 1, 2, . , K. The difference is that MMV involves identical measurement matrices whereas DS allows different matrices for different measurement instances. It has been recognized that DS works better than MMV empirically. However, the quantification of the performance difference is not available in the literature. Our contribution is to quantify the asymptotic performance of MMV and DS in the asymptotic regime that the dimensions of the measurement matrices approach infinity proportionally but the number of measurement instances K remains a constant. The case study and numerical results justify the accuracy of the performance quantification. The analysis technique is based on the state evolution for approximate message passing.
Contribution of TWIK-Related Acid-Sensitive K+ Channel 1 (TASK1) and TASK3 Channels to the Control of Activity Modes in Thalamocortical Neurons

The thalamocortical network is characterized by rhythmic burst activity during natural sleep and tonic single-spike activity during wakefulness. The change between these two activity modes is partially governed by transmitters acting on leak K+ currents in the thalamus, although the nature of the constituting ion channels is not yet known. In the present study, the contribution of members of the two-pore domain K+ channel family to the leak current was investigated using whole-cell patch-clamp techniques and molecular biological techniques. RT-PCR and in situ hybridization revealed the expression of TWIK-related acid-sensitive K+ channel 1 (TASK 1) and TASK3 channels in the rat dLGN. Voltage-clamp recordings of thalamocortical relay neurons in slice preparations demonstrated the existence of a current component sensitive to the TASK channel blocker bupivacaine, which reversed at the presumed K+ equilibrium potential, showed outward rectification, and contributed ∼40% to the standing outward current at depolarized values of the membrane potential (-28 mV). The pharmacological profile was indicative of TASK channels, in that the current was sensitive to changes in extracellular pH, reduced by muscarine and increased by halothane, and these effects were occluded by a near-maximal action of bupivacaine. Pharmacological manipulation of this current under current-clamp conditions resulted in a shift between burst and tonic firing modes. It is concluded that TASK1 and TASK3 channels contribute to the muscarine- and halothane-sensitive conductance in thalamocortical relay neurons, thereby contributing to the change in the activity mode of thalamocortical networks observed during the sleep-wake cycle and on application of inhalational anesthetics.
Broadband Quasi-periodic Radio and X-Ray Pulsations in a Solar Flare

We describe microwave and hard X-ray observations of strong quasi-periodic pulsations from the GOES X1.3 solar flare on 2003 June 15. The radio observations were made jointly by the Owens Valley Solar Array (OVSA), the Nobeyama Polarimeter (NoRP), and the Nobeyama Radioheliograph (NoRH). Hard X-ray observations were made by RHESSI. Using Fourier analysis, we study the frequency- and energy-dependent oscillation periods, differential phase, and modulation amplitudes of the radio and X-ray pulsations. Focusing on the more complete radio observations, we also examine the modulation of the degree of circular polarization and of the radio spectral index. The observed properties of the oscillations are compared with those derived from two simple models for the radio emission. In particular, we explicitly fit the observed modulation amplitude data to the two competing models. The first model considers the effects of MHD oscillations on the radio emission. The second model considers the quasi-periodic injection of fast electrons. We demonstrate that quasi-periodic acceleration and injection of fast electrons is the more likely cause of the quasi-periodic oscillations observed in the radio and hard X-ray emission, which has important implications for particle acceleration and transport in the flaring sources.
Gender-Specific Modulation of the Response to Arterial Injury by Soluble Guanylate Cyclase α1

Objective: Soluble guanylate cyclase (sGC), a heterodimer composed of α and β subunits, synthesizes cGMP in response to nitric oxide (NO). NO modulates vascular tone and structure but the relative contributions of cGMP-dependent versus cGMP-independent mechanisms remain uncertain. We studied the response to vascular injury in male (M) and female (F) mice with targeted deletion of exon 6 of the sGCα1 subunit (sGCα1-/-), resulting in a non-functional heterodimer. Methods: We measured aortic cGMP levels and mRNA transcripts encoding sGC α1, α2, and β1 subunits in wild type (WT) and sGCa1-/- mice. To study the response to vascular injury, BrdU-incorporation and neointima formation (maximum intima to media (I/M) ratio) were determined 5 and 28 days after carotid artery ligation, respectively. Results: Aortic cGMP levels were 4-fold higher in F than in M mice in both genotypes, and, within each gender, 4-fold higher in WT than in sGCa1-/-. In contrast, sGCα1, sGCα2, and sGCβ1 mRNA expression did not differ between groups. 3H-thymidine incorporation in cultured sGCa1-/- smooth muscle cells (SMC) was 27%±12% lower than in WT SMC and BrdU-incorporation in carotid arteries 5 days after ligation was significantly less in sGCa1-/- M than in WT M. Neointima area and I/M 28 days after ligation were 65% and 62% lower in sGCa1-/- M than in WT M mice (p<0,05 for both) but were not different in F mice. Conclusion: Functional deletion of sGCa1 resulted in reduced cGMP levels in male sGCa1-/- mice and a gender-specific effect on the adaptive response to vascular injury.
The Regulation of Reactive Oxygen Species Production during Programmed Cell Death

Reactive oxygen species (ROS) are thought to be involved in many forms of programmed cell death. The role of ROS in cell death caused by oxidative glutamate toxicity was studied in an immortalized mouse hippocampal cell line (HT22). The causal relationship between ROS production and glutathione (GSH) levels, gene expression, caspase activity, and cytosolic Ca2+ concentration was examined. An initial 5–10-fold increase in ROS after glutamate addition is temporally correlated with GSH depletion. This early increase is followed by an explosive burst of ROS production to 200–400-fold above control values. The source of this burst is the mitochondrial electron transport chain, while only 5–10% of the maximum ROS production is caused by GSH depletion. Macromolecular synthesis inhibitors as well as Ac-YVAD-cmk, an interleukin 1β–converting enzyme protease inhibitor, block the late burst of ROS production and protect HT22 cells from glutamate toxicity when added early in the death program. Inhibition of intracellular Ca2+ cycling and the influx of extracellular Ca2+ also blocks maximum ROS production and protects the cells. The conclusion is that GSH depletion is not sufficient to cause the maximal mitochondrial ROS production, and that there is an early requirement for protease activation, changes in gene expression, and a late requirement for Ca2+ mobilization.
Droplets walking in a rotating frame: from quantized orbits to multimodal statistics

Abstract We present the results of an experimental investigation of a droplet walking on the surface of a vibrating rotating fluid bath. Particular attention is given to demonstrating that the stable quantized orbits reported by Fort et al. (Proc. Natl Acad. Sci., vol. 107, 2010, pp. 17515–17520) arise only for a finite range of vibrational forcing, above which complex trajectories with multimodal statistics arise. We first present a detailed characterization of the emergence of orbital quantization, and then examine the system behaviour at higher driving amplitudes. As the vibrational forcing is increased progressively, stable circular orbits are succeeded by wobbling orbits with, in turn, stationary and drifting orbital centres. Subsequently, there is a transition to wobble-and-leap dynamics, in which wobbling of increasing amplitude about a stationary centre is punctuated by the orbital centre leaping approximately half a Faraday wavelength. Finally, in the limit of high vibrational forcing, irregular trajectories emerge, characterized by a multimodal probability distribution that reflects the persistent dynamic influence of the unstable orbital states.
A Cohort Historical Analysis of the Relationship between Thyroid Hormone Malady and Alpha-Human Herpesvirus Activation

Background A number of physiological factors have been suggested to participate in the alpha- Human Herpesvirus (αHHV) reactivation, such as hormonal aberration. Thyroid hormone (TH) was shown to play a suppressive role in Herpes Simplex Virus Type-1 (HSV-1) gene expression and replication in cell culture and animal models. We hypothesize that reactivation of αHHV in humans may be due to, at least in part, by TH status. Methods Prior to implementing a full-scale population-based prospective inquiry into this hypothesis, a pilot study using a medical claims data base and a case-controlled, retrospective cohort investigation was conducted to develop a hypothetical link between TH complication and αHHV reactivation. Using diagnostic codes for treating thyroid disorders and αHHV infections as proxies for biologic/clinic outcomes, we queried a large, comprehensive hospital data base to construct two patient cohorts: Cohort 1 was comprised of patients receiving TH diagnoses over a twelve-year period, and Cohort 2 was composed of patients not receiving TH diagnoses during this period. Diagnoses of αHHV were recorded for each cohort and the difference in the frequency was examined for statistical significance. Demographic analyses such as age, gender, etc were also performed. Results Using 2×2 contingency table analyses and Statistical Analysis Software (SAS), an Odds Ratio (OR) of 2.83 was observed for the total population of 21 years old and above with a chi-square of 61.55 and p < 0.001, confirming that a severe significant difference was found between these two cohorts. This result suggested that patients with αHHV diagnosis have higher chances to have TH disorders. Additional investigation revealed that female were at higher/significant probability to have both TH and αHHV diagnosis, indicating a link of αHHV reactivation to a complex hormonal profile difference between genders. Our observation indicated that female patients of 21 years of age and above exhibited a very high incidence (OR of 3.40, p < 0.001) compared to the male groups (OR of 1.91, p < 0.05), indicating the possibility that hormonal alteration in females maybe transient but robust and can lead to αHHV reactivation more often than the males. Conclusion These results indicated that TH dysfunction may have implication in αHHV pathogenesis and females exhibited much higher probability to suffer αHHV reactivation due to TH disruption. Although the results from this pilot study have limitations and require additional controlled clinical examination such as more detailed patient records, lab data, therapeutic outcome, etc, it provides a tool to assess the effects of hormone imbalance on virus reactivation by retrospective analyses using existing large scale data base.
Fasting versus nonfasting triglycerides and the prediction of cardiovascular risk: do we need to revisit the oral triglyceride tolerance test?

Historically, triglycerides have been measured in the fasting state for 2 reasons. First, because of the marked increase in triglycerides after fat ingestion, the variability in triglyceride measurements is much smaller in the fasting state. Second, before the availability of direct assays for LDL cholesterol (LDL-C),1 estimation of LDL-C was performed in clinical practice almost exclusively by use of the Friedewald equation, which requires that both the HDL-C concentration and the fasting triglyceride concentration divided by 5 be subtracted from the total cholesterol concentration. The recommendations to measure triglycerides in the fasting state did not, however, derive from a consistent set of prospective cohort studies showing that fasting concentrations were superior to nonfasting concentrations for the detection of cardiovascular risk. Instead, following screening guidelines, most epidemiologic investigations simply relied on fasting triglycerides. Taken as a whole, such studies indicate that fasting triglycerides are a univariate predictor of vascular disease. Controversy exists, however, regarding the clinical usefulness of fasting triglycerides as an independent predictor of risk, because adjustment for other covariates—in particular HDL-C—markedly decreases both the magnitude and significance of observed epidemiologic effects (1). The extent to which investigators have sought to avoid nonfasting triglycerides as a method for risk detection is evident in a recent metaanalysis that limited evaluation only to those epidemiologic studies that measured fasting triglycerides, specifically “to exclude the possibility of postprandial effects” (2). Is it possible, then, that recommendations to measure triglycerides in the fasting state have systematically underestimated the impact of hypertriglyceridemia in clinical practice? Atherosclerosis has long been hypothesized to be a disorder influenced by postprandial effects. As early as 1950, J. R. Moreton, writing in the Journal of Laboratory and Clinical Medicine , suggested a linkage between chylomicronemia, fat tolerance, and atherosclerosis (3). A major source of circulating triglycerides is dietary …