Miracle-dz/UniFAR-FTUs huggingface dataset:
Nucleosome scaffolding by Brd4 tandem bromodomains in acetylation-dependent chromatin compartmentalization

Bromodomain binding of acetyl-lysine residues is a crucial step in many epigenetic mechanisms governing transcription. Nearly half of human bromodomains exist in tandem with at least one other bromodomain on a single protein. The Bromodomain and ExtraTerminal domain (BET) familyof proteins (BrdT, Brd2, Brd3 and Brd4) each encode two bromodomains at their N-termini and are important regulators of acetylation-dependent transcription in homeostasis and disease. Previous efforts have focused on identifying protein acetylation sites bound by individual bromodomains. However, the mechanisms through which tandem bromodomains act cooperatively on chromatin are largely unknown. Here, we first used small angle x-ray scattering combined with Rosetta ab initio modeling to explore conformational space available to BET tandem bromodomains. For Brd4, the flexible tandem bromodomain linker allows for distances between the two acetyl-lysine binding sites ranging from 15 to 157 Å. Using a bioluminescence resonance energy transfer assay, we show a clear distance dependence for Brd4 tandem bromodomain bivalent binding of multiply acetylated histone H4 peptides. However, isothermal titration calorimetry studies revealed Brd4 binding affinity toward multiply acetylated peptides does not correlate with the potential for bivalent binding. We used sucrose gradient assays to provide direct evidence in vitro that Brd4 tandem bromodomains can simultaneously bind and scaffold multiple acetylated nucleosomes. Intriguingly, our bioinformatic analysis of deposited chromatin immunoprecipitation sequencing data indicates that Brd4 colocalizes with subsets of histone acetyl-lysine sites across transcriptionally active chromatin compartments. These findings support our hypothesis that scaffolding of acetylated nucleosomes by Brd4 tandem bromodomains contributes to higher-order chromatin architecture.
Multivariate analysis of EEG activity indexes contingent and non-contingent attentional capture

It is well known that salient yet irrelevant singleton can capture attention, even when this is inconsistent with the current goals of the observer (Theeuwes, 1992; 2010). Others however have claimed that capture is critically contingent on the goals of the observer: Capture is strongly modulated (or even eliminated) when the irrelevant singleton does not match the target-defining properties (Folk, Remington, & Johnston, 1992). There has been a long-standing debate on whether attentional capture can be explained by goal-driven and/or stimulus-driven accounts. Here, we shed further light on this phenomenon by using EEG activity (raw EEG and alpha power) to provide a time-resolved index of attentional orienting. Participants searched for a target defined by a pre-specified color. The search display was preceded by a singleton cue that either matched the color of the upcoming target (contingent cues), or that appeared in an irrelevant color (non-contingent cues). Multivariate analysis of raw EEG and alpha power revealed preferential tuning to the location of both contingent and non-contingent cues, with a stronger bias towards contingent than non-contingent cues. The time course of these effects, however, depended on the neural signal. Raw EEG data revealed attentional orienting towards the cue early on in the trial (>156 ms), while alpha power revealed sustained spatial selection in the cued locations at a later moment in the trial (>250 ms). Moreover, while raw EEG showed stronger capture by contingent cues during this early time window, the advantage for contingent cues arose during a later time window in alpha band activity. Thus, our findings suggest that raw EEG activity and alpha-band power tap into distinct neural processes that index movements of covert spatial attention. Both signals provide clear neural evidence that both contingent and non-contingent cues can capture attention, and that this process is robustly shaped by the target-defining properties in the current block of trials.
Water motion and vegetation control the pH dynamics in seagrass‐dominated bays

Global oceanic pH is lowering, which is causing great concern for the natural functioning of marine ecosystems. Current pH predictions are based on open ocean models; however, coastal zones are dynamic systems with seawater pH fluctuating temporally and spatially. To understand how coastal ecosystems will respond in the future, we first need to quantify the extent that local processes influence the pH of coastal zones. With this study, we show that over a single diurnal cycle, the total pH can fluctuate up to 0.2 units in a shallow seagrass‐dominated bay, driven by the photosynthesis and respiration of the vegetation. However, these biologically controlled pH fluctuations vary significantly over small distances. Monitoring conducted at neighboring sites with contrasting hydrodynamic regimes highlights how water motion controls the extent that the local pH is altered by the metabolism of vegetation. The interactive effects of hydrodynamics and vegetation were further investigated with an in situ experiment, where the hydrodynamics were constrained and thus the local water residence time was increased, displaying the counteractive effect of hydrodynamics on the pH change caused by vegetation. With this research, we provide detailed in situ evidence of the spatial variation of pH within marine ecosystems, highlighting the need to include hydrodynamic conditions when assessing the pH‐effects of vegetation, and identifying potential high‐pH refuges in a future low pH ocean.
IMPLICIT AND EXPLICIT CAPTURE OF ATTENTION: WHAT IT TAKES TO BE NOTICED A thesis submitted in partial fulfilment of the requirements for the Degree of Master of Arts in Psychology

5 Introduction . 6 Inattentional Blindness . 6 Inattentional Blindness and Perceptual Load. 9 Capturing Attention . 10 Capturing Attention without Awareness. 11 How to Capture Attention . 17 Meaning and the Capture of Attention. 22 The Perceptual Cycle . 24 Aims of the Research. 26 Experiment 1. 28 Method . 28 Participants. 28 Apparatus . 29 Stimuli and Design . 29 Procedure . 31 Results . 32 Data . 32 Explicit Perception. 32 Implicit Perception. 34 Discussion . 39 Experiment 2. 41 Method . 41 Participants. 41 Apparatus . 42 Stimuli and Design . 42 Procedure . 43 Results . 44 Data . 44 Explicit Perception. 45 Implicit Perception. 46 Discussion . 47 General Discussion. 48 The Mechanisms of Attention . 51 Unconscious Perception. 55 Attention and Meaning . 57 The Perceptual Cycle . 58 Conclusions . 60 References . 62 Appendix: Word stem data for individual words in Experiment 2. 67
AC-TR-18-009 December 2018 AModel for Finding Transition-Minors

The well known cycle double cover conjecture in graph theory is strongly related to the compatible circuit decomposition problem. A recent result by Fleischner et al. (2018) gives a sufficient condition for the existence of a compatible circuit decomposition in a transitioned 2-connected Eulerian graph, which is based on an extension of the definition of K5-minors to transitioned graphs. Graphs satisfying this condition are called SUD-K5-minor-free graphs. In this work we formulate a generalization of this property by replacing the K5 by a 4-regular transitioned graph H, which is part of the input. Furthermore, we consider the decision problem of checking for two given graphs if the extended property holds. We prove that this problem is NPcomplete and fixed parameter tractable with the size of H as parameter. We then formulate an equivalent problem, present a mathematical model for it, and prove its correctness. This mathematical model is then translated into a mixed integer linear program (MIP) for solving it in practice. Computational results show that the MIP formulation can be solved for small instances in reasonable time. In our computations we found snarks with perfect matchings whose contraction leads to SUD-K5-minor-free graphs that contain K5-minors. Furthermore, we verified that there exists a perfect pseudo-matching whose contraction leads to a SUD-K5-minor-free graph for all snarks with up to 22 vertices.
Implants Straumann TPS / SLA : Evaluation radiologique à 5-6 ans de résultats obtenus en pratique privée

La réhabilitation implantaire est maintenant considérée comme un excellent traitement, avec peu de complications biologiques et prothétiques. Depuis les études initiales de Bränemark et al. (1985), les implants dentaires sont devenus le traitement de choix pour réhabiliter les espaces édentés. Les études longitudinales faites par Adell et al. (1981, 1985) ont confirmé la fiabilité de cette technique de réhabilitation prothétique. Des critères pour évaluer le taux de succès ont été progressivement adoptés afin de pouvoir comparer les résultats fournis par les différentes études. La perte osseuse autour des implants mis en charge est en moyenne inférieure à 1mm lors de la première année et à 0,2mm par an pour les années suivantes. D'autres paramètres comme le degré d'inflammation, l'absence de mobilité, le retrait gingival, la profondeur de la poche et l'absence de radio-transparence périimplantaire représentent également des critères pour évaluer le taux de succès. GHEDDAF DAM, Hamasat. Implants Straumann TPS/SLA: Evaluation radiologique à 5-6 ans de résultats obtenus en pratique privée. Thèse de doctorat : Univ. Genève, 2009, no.
Association Studies for Yield and Yield Components in Maize (Zea mays L.) Inbred Lines

Maize (Zea mays L.) occupies a prominent position in global agriculture and is an important cereal crop of India. Maize is used as human food, animal feed and industrial raw materials and also used as source for more number of industrial products. Grain yield is a complex quantitative trait that depends on a number of factors. Thus, knowledge of interrelationships between grain yield and its contributing components will improve the efficiency of breeding programs through the use of appropriate selection indices. Studies on correlation coefficients of different plant characters are useful criterion to identify desirable traits that contribute to improve the dependent variable. Correlation coefficient is one of the important biometrical tools for formulating a selection index as it reveals the strength of relationship among the group of characters. This also helps to decide the International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 8 Number 07 (2019) Journal homepage: http://www.ijcmas. com
Metatranscriptomic Analyses of Diel Metabolic Functions During a Microcystis Bloom in Western Lake Erie (United States)

This study examined diel shifts in metabolic functions of Microcystis spp. during a 48-h Lagrangian survey of a toxin-producing cyanobacterial bloom in western Lake Erie in the aftermath of the 2014 Toledo Water Crisis. Transcripts mapped to the genomes of recently sequenced lower Great Lakes Microcystis isolates showed distinct patterns of gene expression between samples collected across day (10:00 h, 16:00 h) and night (22:00 h, 04:00 h). Daytime transcripts were enriched in functions related to Photosystem II (e.g., psbA), nitrogen and phosphate acquisition, cell division (ftsHZ), heat shock response (dnaK, groEL), and uptake of inorganic carbon (rbc, bicA). Genes transcribed during nighttime included those involved in phycobilisome protein synthesis and Photosystem I core subunits. Hierarchical clustering and principal component analysis (PCA) showed a tightly clustered group of nighttime expressed genes, whereas daytime transcripts were separated from each other over the 48-h duration. Lack of uniform clustering within the daytime transcripts suggested that the partitioning of gene expression in Microcystis is dependent on both circadian regulation and physicochemical changes within the environment.
Phenome-wide and genome-wide analyses of quality of life in schizophrenia

Background Schizophrenia negatively affects quality of life (QoL). A handful of variables from small studies have been reported to influence QoL in patients with schizophrenia, but a study comprehensively dissecting the genetic and non-genetic contributing factors to QoL in these patients is currently lacking. Aims We adopted a hypothesis-generating approach to assess the phenotypic and genotypic determinants of QoL in schizophrenia. Method The study population comprised 1119 patients with a psychotic disorder, 1979 relatives and 586 healthy controls. Using linear regression, we tested >100 independent demographic, cognitive and clinical phenotypes for their association with QoL in patients. We then performed genome-wide association analyses of QoL and examined the association between polygenic risk scores for schizophrenia, major depressive disorder and subjective well-being and QoL. Results We found nine phenotypes to be significantly and independently associated with QoL in patients, the most significant ones being negative (β = −1.17; s.e. 0.05; P = 1 × 10–83; r2 = 38%), depressive (β = −1.07; s.e. 0.05; P = 2 × 10–79; r2 = 36%) and emotional distress (β = −0.09; s.e. 0.01; P = 4 × 10–59, r2 = 25%) symptoms. Schizophrenia and subjective well-being polygenic risk scores, using various P-value thresholds, were significantly and consistently associated with QoL (lowest association P-value = 6.8 × 10–6). Several sensitivity analyses confirmed the results. Conclusions Various clinical phenotypes of schizophrenia, as well as schizophrenia and subjective well-being polygenic risk scores, are associated with QoL in patients with schizophrenia and their relatives. These may be targeted by clinicians to more easily identify vulnerable patients with schizophrenia for further social and clinical interventions to improve their QoL.
Board independence, sub-committee independence and firm performance: evidence from Australia

This study investigates whether the monitoring of company management by an independent board of directors serves to enhance firm performance in Australia. The paper explores in detail the impact of the level of independence of the main board and sub-committees including audit, remuneration and nomination on performance in a sample of 250 listed companies. From the perspective of a regulator, the study’s findings have implications and suggest that an independent main board produces superior results. The shareholding of independent directors is also found to negatively impact performance for this data, suggesting that their role as independent arbiter is restricted by shareholding. Interestingly, the returns to firm performance engendered by independence did not extend to the composition of sub-committees, where the presence of outside directors did not significantly influence performance.
Co-Movements between Carbon, Energy and Financial Markets: A Multivariate GARCH Approach

Liberalization of energy sector and the ensuing creation of new markets for carbon emissions have increasingly triggered a need for understanding the volatility and correlation structure between carbon, energy and financial markets. This paper documents the existence of structural changes in correlation patterns among these markets and links the changes to market conditions. We apply a (double) smooth transition conditional correlation ((D)STCC) GARCH model to a set of EU emission allowance futures, energy futures and financial asset returns to investigate the conditional correlation dynamics during the period 2005-2011. The model allows correlation to vary smoothly between extreme states and the dynamics are driven by a transition variable. We use, on the one hand, time as transition variable which allows the correlation level to change over time and the VSTOXX index, on the other hand, to account for uncertainty and volatility in markets. The effects of news on the covariances are examined through news impact surfaces. The results point to a considerable increase of correlations between carbon and energy markets in recent years. We further find higher and more variable correlations between emission allowance futures and financial asset returns during the current financial crisis, predicted by higher expected stock market volatility.
Analyse zur globalen Genexpression in Geweben des frühen Arabidopsis thaliana Embryos

Early embryogenesis is the critical developmental phase during which the basic features of the plant body are established: the apical-basal axis of polarity, different tissue layers, and both the root pole and the shoot pole. Polarization of the zygote correlates with the generation of apical and basal (embryonic and extraembryonic) cell fates. Whereas mechanisms of zygote polarization are still largely unknown, distinct expression domains of WOX family transcription factors as well as directional auxin transport and local auxin response are known to be involved in early apical-basal patterning. Radial patterning of tissue layers appears to be mediated by cell-cell communication involving both peptide signaling and transcription factor movement. Although the initiation of the shoot pole is still unclear, the apical organization of the embryo depends on both the proper establishment of transcription factor expression domains and, for cotyledon initiation, upward auxin flow in the protoderm. Here we focus on the essential patterning processes, drawing mainly on data from Arabidopsis thaliana and also including relevant data from other species if available.
Forward modelling to determine the observational signatures of propagating slow waves for TRACE, SoHO/CDS, and Hinode/EIS

Context. The propagation and damping of slow MHD waves in the solar atmosphere are investigated by numerical simulations and forward modelling, with particular emphasis placed on waves with periodicities of the order of five minutes. Aims. We extend a coronal model by adding an equilibrium temperature gradient allowing study of wave propagation from the transition region to the corona. Methods. A ID model is used that includes gravitational stratification and damping by thermal conduction, optically thin radiation, and compressive viscosity. Forward modelling of the simulation results, for both uniform and non-uniform equilibrium temperature profiles, is undertaken to establish the observational consequences of the physical processes involved for TRACE, SoHO/CDS, and Hinode/EIS. Results. The presence of thermal conduction causes a phase shift between the wave velocity, energy, and density. This shift may be observable by comparing Doppler velocity and intensity observations. Phase shifts are also seen between intensity observations by different instruments and between different spectral lines. This is an observational effect that arises due to the forward modelling process in which observations are synthesised, but it is not seen in the simulation results. Oscillations from the transition region are found to dominate the coronal emission for TRACE 171 A by nearly two orders of magnitude.
The maximizing mind-set

Getting the best has been advocated as an ideal in almost every domain of life. We propose that maximizing constitutes a mind-set that may be situationally activated and has cross-domain consequences. Specifically, we show that the maximizing mind-set amplifies regret and dissatisfaction, increases the likelihood of returning and switching products, and affects sensory experiences such as taste. The effect of the maximizing mind-set occurs only when consumers learn that they do not get the best but not when they do in fact get the best. We validate our conception of the maximizing mind-set by demonstrating its embrace of underlying processes of comparisons and goals.
Contact mechanics: contact area and interfacial separation from small contact to full contact

We present a molecular dynamics study of the contact between a rigid solid with a randomly rough surface and an elastic block with a flat surface. The numerical calculations mainly focus on the contact area and the interfacial separation from small contact (low load) to full contact (high load). For a small load the contact area varies linearly with the load and the interfacial separation depends logarithmically on the load. For a high load the contact area approaches the nominal contact area (i.e. complete contact), and the interfacial separation approaches zero. The numerical results have been compared with analytical theory and experimental results. They are in good agreement with each other. The present findings may be very important for soft solids, e.g. rubber, or for very smooth surfaces, where complete contact can be reached at moderately high loads without plastic deformation of the solids.
Structural Variability of Subtelomeres Applied for Genotyping of Selected Potato Varieties

Subtelomeric regions reveal a relatively high degree of polymorphism due to the increased frequency of recombination events in these chromosome loci. In a search for molecular markers applicable to genotyping of potato varieties, we focused on two possible sources of polymorphism occurring in this region: (i) arrangement of blocks of subtelomeric chromatin; (ii) structure of telomere-subtelomere boundary. Analysis of the internal arrangement of subtelomeric sequences showed several types of cultivar-specific spectra of PCR products aris- ing from the variant orientation of sequence units of the ST3-subtelomeric sequence, or from different lengths of regions linking the individual sequence units. Further, the telomere-subtelomere boundary sequences were amplified using telomeric and ST3-specific primers and the obtained products were cloned. Sequence analysis of the clones resulted in characterisation of a novel telomere-associated sequence (FIN2). Primers derived from this sequence were then used alone or in combination with telomeric or ST3-specific primers to generate cultivar- specific spectra of PCR products. The described combinations of sequence-specific primers may be used for the fast, cheap and reproducible PCR-genotyping of selected potato varieties.
Microfinance and womens empowerment: rethinking "best practice."

In the 1990s microfinance targeting women became a major focus of gender policy in many donor agencies. Literature prepared for the 1997 Microcredit Summit donor policy documents and NGO funding proposals all present an extremely attractive vision of increasing numbers of expanding financially self-sustainable microfinance programmes reaching large numbers of women borrowers. Through their contribution to women’s ability to earn an income these programmes are assumed to initiate a series of ‘virtuous spirals’ of economic empowerment increased well-being for women and their families and wider social and political empowerment. However more recently as the findings of research and experience have filtered through this initial enthusiasm is being replaced by scepticism. Here it is argued that although the widespread complacency about the automatic benefits of microfinance for women needs to be questioned the shortcomings of existing practice should stimulate the search for improvement and innovation rather than provide the basis for cynical inaction. It is not microfinance per se which is the problem but the ways in which ‘best practice’ has become dominated by concerns of financial sustainability. Innovations in some programmes point to a range of ways in which microfinance’s contribution to empowerment can be increased as part of a broader strategy for gender transformation. (excerpt)