Stress Level Detection and Evaluation from Phonation and PPG Signals Recorded in an Open-Air MRI Device

This paper deals with two modalities for stress detection and evaluation—vowel phonation speech signal and photo-plethysmography (PPG) signal. The main measurement is carried out in four phases representing different stress conditions for the tested person. The first and last phases are realized in laboratory conditions. The PPG and phonation signals are recorded inside the magnetic resonance imaging scanner working with a weak magnetic field up to 0.2 T in a silent state and/or with a running scan sequence during the middle two phases. From the recorded phonation signal, different speech features are determined for statistical analysis and evaluation by the Gaussian mixture models (GMM) classifier. A database of affective sounds and two databases of emotional speech were used for GMM creation and training. The second part of the developed method gives comparison of results obtained from the statistical description of the sensed PPG wave together with the determined heart rate and Oliva–Roztocil index values. The fusion of results obtained from both modalities gives the final stress level. The performed experiments confirm our working assumption that a fusion of both types of analysis is usable for this task—the final stress level values give better results than the speech or PPG signals alone.

Measuring the buffering capacity of gene silencing in Saccharomyces cerevisiae

Gene silencing in budding yeast is mediated by Sir protein binding to unacetylated nucleosomes to form a chromatin structure that inhibits transcription. Transcriptional silencing is characterized by the high-fidelity transmission of the silent state. Despite its relative stability, the constituent parts of the silent state are in constant flux, giving rise to a model that silent loci can tolerate such fluctuations without functional consequences. However, the level of tolerance is unknown, and we developed methods to measure the threshold of histone acetylation that causes the silent chromatin state to switch to the active state as well as to measure the levels of the enzymes and structural proteins necessary for silencing. We show that loss of silencing required 50 to 75% acetyl-mimic histones, though the precise levels were influenced by silencer strength and upstream activating sequence (UAS) enhancer/promoter strength. Measurements of repressor protein levels necessary for silencing showed that reducing SIR4 gene dosage two- to threefold significantly weakened silencing, though reducing the gene copy numbers for Sir2 or Sir3 to the same extent did not significantly affect silencing suggesting that Sir4 was a limiting component in gene silencing. Calculations suggest that a mere twofold reduction in the ability of acetyltransferases to acetylate nucleosomes across a large array of nucleosomes may be sufficient to generate a transcriptionally silent domain.

‘Poor, pale, Rusalka’: The Polymorphic Nature of the Heroine of Dvořák’s Rusalka

<p>Rusalka, the protagonist of Antonín Dvořák’s eponymous opera, is probably one of the most unique operatic heroines. Rusalka’s burning desire to become human in order to be with one and have a soul takes her on an interesting, yet tragic journey. From water nymph to human to will-o-the-wisp, Rusalka goes through three different states and two metamorphoses that leave her desire unfulfilled and cause her to suffer continuously. The two metamorphoses cause Rusalka to remain between the natural and human worlds, both of which reject her. This in turn leads to her eternal suffering. Her tragic fate and constant agony portray her as a victim. And yet Rusalka is also a powerful character who is in command of her own story: as the opera’s sole protagonist, we are encouraged to identify with her perspective. She is constantly present throughout the opera. Even in the scenes that do not require her presence, she communicates with us through absence and through other characters that are, like us, influenced by her presence. And when Rusalka is silent, she connects with us through the language of orchestral music; her mute exterior on stage eludes us and seeks our understanding and sympathy. Thus, her powerful presence and the complexity of her nature draw us as the readers/listeners/spectators to experience Rusalka’s story through her subjective perspective. In order to reveal the nature of the character and how it affects us as readers/listeners/spectators, I will use various approaches, with an emphasis on psychological concepts that will provide a new insight into Rusalka and the opera as a whole. My research will also suggest the impact of fin-desiècle misogyny on Rusalka and specifically her silence, which is the perhaps the most intriguing aspect of the opera and its protagonist. The thesis will follow Rusalka’s journey, from the time and culture of its creation to modern times, as portrayed in some of the more recent dramatic productions that resituate these themes in light of more current perspectives. I will expose in turn the layers in Rusalka: from the libretto and the music, to the use of voice, and finally the playing with meaning in a few representative stage productions. In the second and third chapters, focusing on the libretto and music respectively, I discuss the ways Rusalka articulates her nature, using the Freudian structural model of the psyche for the analysis of the narrative and repetition in the libretto and music. The analysis of music also points toward repetition as a key method, and I suggest connections with the psychological concept of repetition, linked with desire and the death drive, as observed by Slavoj Žižek and Renata Salecl. In the fourth chapter, I focus on the voice, more specifically the cry, in order to explore the ways in which we experience the voice, which I believe is the central element that causes a painful enjoyment (jouissance) in some of us, and in turn is key to our sympathetic empathy with Rusalka. Finally, with Rusalka on stage, I explore the ways in which we, as audience, relate to Rusalka’s suffering, focusing mainly on her silent state. With the addition of the layer of the gaze, I focus on the spectators’ reaction to mute Rusalka and how, in a way, they participate in these moments of suffering precisely through the gaze. Throughout the thesis, I demonstrate how Rusalka communicates with us through the opera’s layers and how in return we respond to them, either by sympathising or identifying with the protagonist.</p>

‘Poor, pale, Rusalka’: The Polymorphic Nature of the Heroine of Dvořák’s Rusalka

<p>Rusalka, the protagonist of Antonín Dvořák’s eponymous opera, is probably one of the most unique operatic heroines. Rusalka’s burning desire to become human in order to be with one and have a soul takes her on an interesting, yet tragic journey. From water nymph to human to will-o-the-wisp, Rusalka goes through three different states and two metamorphoses that leave her desire unfulfilled and cause her to suffer continuously. The two metamorphoses cause Rusalka to remain between the natural and human worlds, both of which reject her. This in turn leads to her eternal suffering. Her tragic fate and constant agony portray her as a victim. And yet Rusalka is also a powerful character who is in command of her own story: as the opera’s sole protagonist, we are encouraged to identify with her perspective. She is constantly present throughout the opera. Even in the scenes that do not require her presence, she communicates with us through absence and through other characters that are, like us, influenced by her presence. And when Rusalka is silent, she connects with us through the language of orchestral music; her mute exterior on stage eludes us and seeks our understanding and sympathy. Thus, her powerful presence and the complexity of her nature draw us as the readers/listeners/spectators to experience Rusalka’s story through her subjective perspective. In order to reveal the nature of the character and how it affects us as readers/listeners/spectators, I will use various approaches, with an emphasis on psychological concepts that will provide a new insight into Rusalka and the opera as a whole. My research will also suggest the impact of fin-desiècle misogyny on Rusalka and specifically her silence, which is the perhaps the most intriguing aspect of the opera and its protagonist. The thesis will follow Rusalka’s journey, from the time and culture of its creation to modern times, as portrayed in some of the more recent dramatic productions that resituate these themes in light of more current perspectives. I will expose in turn the layers in Rusalka: from the libretto and the music, to the use of voice, and finally the playing with meaning in a few representative stage productions. In the second and third chapters, focusing on the libretto and music respectively, I discuss the ways Rusalka articulates her nature, using the Freudian structural model of the psyche for the analysis of the narrative and repetition in the libretto and music. The analysis of music also points toward repetition as a key method, and I suggest connections with the psychological concept of repetition, linked with desire and the death drive, as observed by Slavoj Žižek and Renata Salecl. In the fourth chapter, I focus on the voice, more specifically the cry, in order to explore the ways in which we experience the voice, which I believe is the central element that causes a painful enjoyment (jouissance) in some of us, and in turn is key to our sympathetic empathy with Rusalka. Finally, with Rusalka on stage, I explore the ways in which we, as audience, relate to Rusalka’s suffering, focusing mainly on her silent state. With the addition of the layer of the gaze, I focus on the spectators’ reaction to mute Rusalka and how, in a way, they participate in these moments of suffering precisely through the gaze. Throughout the thesis, I demonstrate how Rusalka communicates with us through the opera’s layers and how in return we respond to them, either by sympathising or identifying with the protagonist.</p>

Quantitative analysis of Histone modifications in gene silencing

Gene silencing in budding yeast is mediated by Sir protein binding to unacetylated nucleosomes to form a chromatin structure that inhibits transcription. This transcriptional silencing is characterized by the high-fidelity transmission of the silent state. Despite its relative stability, the constituent parts of the silent state are in constant flux giving rise to a model that silent loci can tolerate such fluctuations without functional consequences. However, the level of tolerance is unknown and we developed a method to measure the threshold of histone acetylation that causes the silent chromatin state to switch to the active state. We show that loss of silencing required between 50% and 75% of the unacetylated histones to be replaced with acetylated histone mimics. The precise levels of unacetylated nucleosomes required varied from locus to locus and was influenced by both silencer strength and UAS enhancer/promoter strength. Simple calculations suggest that an approximately 50% reduction in the ability of acetylases to acetylate individual nucleosomes across a large domain may be sufficient to generate a transcriptionally silent region in the nucleus.

Impact of Transposable Elements on Methylation and Gene Expression across Natural Accessions of Brachypodium distachyon

Transposable elements (TEs) constitute a large fraction of plant genomes and are mostly present in a transcriptionally silent state through repressive epigenetic modifications, such as DNA methylation. TE silencing is believed to influence the regulation of adjacent genes, possibly as DNA methylation spreads away from the TE. Whether this is a general principle or a context-dependent phenomenon is still under debate, pressing for studying the relationship between TEs, DNA methylation, and nearby gene expression in additional plant species. Here, we used the grass Brachypodium distachyon as a model and produced DNA methylation and transcriptome profiles for 11 natural accessions. In contrast to what is observed in Arabidopsis thaliana, we found that TEs have a limited impact on methylation spreading and that only few TE families are associated with a low expression of their adjacent genes. Interestingly, we found that a subset of TE insertion polymorphisms is associated with differential gene expression across accessions. Thus, although not having a global impact on gene expression, distinct TE insertions may contribute to specific gene expression patterns in B. distachyon.

A holistic view on plant effector-triggered immunity presented as an iceberg model

The immune system of plants is highly complex. It involves pattern-triggered immunity (PTI), which is signaled and manifested through branched multi-step pathways. To counteract this, pathogen effectors target and inhibit individual PTI steps. This in turn can cause specific plant cytosolic nucleotide-binding leucine-rich repeat (NLR) receptors to activate effector-triggered immunity (ETI). Plants and pathogens have many genes encoding NLRs and effectors, respectively. Yet, only a few segregate genetically as resistance (R) genes and avirulence (Avr) effector genes in wild-type populations. In an attempt to explain this contradiction, a model is proposed where far most of the NLRs, the effectors and the effector targets keep one another in a silent state. In this so-called “iceberg model”, a few NLR-effector combinations are genetically visible above the surface, while the vast majority is hidden below. Besides, addressing the existence of many NLRs and effectors, the model also helps to explain why individual downregulation of many effectors causes reduced virulence and why many lesion-mimic mutants are found. Finally, the iceberg model accommodates genuine plant susceptibility factors as potential effector targets.

A multi-layered structure of the interphase chromocenter revealed by proximity-based biotinylation

During interphase centromeres often coalesce into a small number of chromocenters, which can be visualized as distinct, DAPI dense nuclear domains. Intact chromocenters play a major role in maintaining genome stability as they stabilize the transcriptionally silent state of repetitive DNA while ensuring centromere function. Despite its biological importance, relatively little is known about the molecular composition of the chromocenter or the processes that mediate chromocenter formation and maintenance. To provide a deeper molecular insight into the composition of the chromocenter and to demonstrate the usefulness of proximity-based biotinylation as a tool to investigate those questions, we performed super resolution microscopy and proximity-based biotinylation experiments of three distinct proteins associated with the chromocenter in Drosophila. Our work revealed an intricate internal architecture of the chromocenter suggesting a complex multilayered structure of this intranuclear domain.

SIRT1/2 orchestrate acquisition of DNA methylation and loss of histone H3 activating marks to prevent premature activation of inflammatory genes in macrophages

Sirtuins 1 and 2 (SIRT1/2) are two NAD-dependent deacetylases with major roles in inflammation. In addition to deacetylating histones and other proteins, SIRT1/2-mediated regulation is coupled with other epigenetic enzymes. Here, we investigate the links between SIRT1/2 activity and DNA methylation in macrophage differentiation due to their relevance in myeloid cells. SIRT1/2 display drastic upregulation during macrophage differentiation and their inhibition impacts the expression of many inflammation-related genes. In this context, SIRT1/2 inhibition abrogates DNA methylation gains, but does not affect demethylation. Inhibition of hypermethylation occurs at many inflammatory loci, which results in more drastic upregulation of their expression upon macrophage polarization following bacterial lipopolysaccharide (LPS) challenge. SIRT1/2-mediated gains of methylation concur with decreases in activating histone marks, and their inhibition revert these histone marks to resemble an open chromatin. Remarkably, specific inhibition of DNA methyltransferases is sufficient to upregulate inflammatory genes that are maintained in a silent state by SIRT1/2. Both SIRT1 and SIRT2 directly interact with DNMT3B, and their binding to proinflammatory genes is lost upon exposure to LPS or through pharmacological inhibition of their activity. In all, we describe a novel role for SIRT1/2 to restrict premature activation of proinflammatory genes.

DOWN state in the anterior cingulate and prelimbic areas in rats during immobility

BackgroundUP-DOWN state is considering as a dominant electrographic pattern during immobility and slow wave sleep. This study is focused on the analysis of spatial distribution and neuronal correlates of the DOWN state in ratsMethodsLocal field potentials and multiunit discharges were recorded bilaterally in the prefrontal cortex (PFC) and hippocampus of non-anesthetized, tethered rats (Sprague Dawley, males, weight 350-400g) with 256 channel, 4 shank silicon probes. We have focused our study on the analysis of the positive wave of slow oscillations (SOs), which is considered as the DOWN (silent) state of the UP-DOWN state in the anterior cingulate (AC), prelimbic (PL) areas of PFC and hippocampus during immobility.ResultsOur experiments showed that SOs occurred intermittently with a mean interval 1.4±0.8 (±SD) seconds. The SOs began with the DOWN state, and they were generated locally within AC or PL areas, or simultaneously in AC, PL and hippocampus bilaterally (generalized SOs). The DOWN state of local SOs in the AC was associated with a decreased rate of multiunit discharges. Similar waves in the PL area were associated with increased multiunit discharges. We observed high speed propagation of generalized SOs that occurred with 3-6ms delay within left and right PFC and less than 10ms delay between the PFC and CA1 area of hippocampus. All generalized SOs were associated with decreased multiunit discharges.ConclusionOur data support the hypothesis that neocortical networks are sufficient to generate focal SOs but the participation of external input is needed for occurrence of generalized SOs.