Miracle-dz/UniFAR-FTUs huggingface dataset:
Cosmological parameter estimation from SN Ia data: a model-independent approach

We perform a model independent reconstruction of the cosmic expansion rate based on type Ia supernova data. Using the Union 2.1 data set, we show that the Hubble parameter behaviour allowed by the data without making any hypothesis about cosmological model or underlying gravity theory is consistent with a flat LCDM universe having H_0 = 70.43 +- 0.33 and Omega_m=0.297 +- 0.020, weakly dependent on the choice of initial scatter matrix. This is in closer agreement with the recently released Planck results (H_0 = 67.3 +- 1.2, Omega_m = 0.314 +- 0.020) than other standard analyses based on type Ia supernova data. We argue this might be an indication that, in order to tackle subtle deviations from the standard cosmological model present in type Ia supernova data, it is mandatory to go beyond parametrized approaches.
A chromatin mark by SETD7 regulates myocardial inflammation in obesity-related heart failure with preserved ejection fraction

Obesity is a major risk factor for heart failure with preserved ejection fraction (HFpEF). Post-translational modification of histones by chromatin modifying enzymes (CMEs) are emerging as pivotal regulators of gene transcription in cardiovascular disease. To investigate the role of chromatin remodelling in obese HFpEF (obHFpEF). Gene expression profiling of CMEs (PCR array) was performed in left ventricular (LV) myocardial specimens from obHFpEF patients and age-matched control donors (n=8/group). Among myocardial CMEs, the methyltransferase SETD7 showed the highest variation in gene expression. Hence, we investigated the role of SETD7 and its chromatin mark H3K4me1 in a murine model of obHFpEF. Mice with cardiomyocyte-specific deletion of SETD7 (c-SETD7−/−) and control littermates (SETD7fl/fl) were subjected to high fat diet feeding and L-NAME treatment for 15 weeks to induce obHFpEF. Echocardiography and Treadmill exhaustion test were performed. ChIP-Seq datasets were employed to determine the biological pathways regulated by SETD7, whereas chromatin immunoprecipitation assays (ChIP) were performed to investigate SETD7/H3k4me1 enrichment on target gene promoters. SETD7 gain- and loss-of-function experiments were performed in cultured neonatal rat ventricular myocytes (NRVMs) exposed to palmitic acid (200μM) for 48h. Selective inhibition of SETD7 by (R)-PFI-2 was performed in skinned cardiomyocytes isolated from left ventricular specimens of obHFpEF patients. Passive stiffness, a main feature of HFpEF, was assessed before and after (R)-PFI-2 treatment. CMEs profiling showed SETD7 as the top-ranking transcript (fold change, 7.36, P<0.01) in myocardial specimens from obHFpEF patients as compared to controls. ChIP-Seq in CMs showed a strong enrichment of SETD7 and H3k4me1 on the promoter of NF-kB p65 gene, a master regulator of inflammation. SETD7 and H3k4me1 were upregulated in HFpEF vs. control mouse hearts, showed enrichment on NF-kB p65 promoter and were associated with IL-1β and IL-6 upregulation. In HFpEF mice, cardiomyocyte-specific deletion of SETD7 protected against LV hypertrophy, diastolic dysfunction (assessed by E/E' ratio) and lung congestion while improving exercise tolerance. At the molecular level, SETD7 deletion blunted H3K4me1 enrichment on p65 promoter thus preventing the upregulation of inflammatory genes and myocardial apoptosis. In cultured CMs exposed to PA, SETD7 inhibition by (R)-PFI-2 prevented H3k4me1-driven p65 upregulation, whereas SETD7 overexpression mimicked HFpEF features. Moreover, knockdown of NF-kB p65 prevented IL-1β/IL-6 transcription in SETD7-overexpressing CMs. Of clinical relevance, (R)-PFI-2 reduced passive stiffness in skinned CMs isolated from obHFpEF patients. Our results unveil a new epigenetic mechanism underpinning inflammation in obHFpEF. Targeting SETD7 may represent a novel therapeutic approach to prevent HFpEF in obesity. Type of funding sources: Public grant(s) – National budget only. Main funding source(s): Swiss National Science Foundation
Constraining the properties of neutron star crusts with the transient low-mass X-ray binary Aql X-1

Aql X-1 is a prolific transient neutron star low-mass X-ray binary that exhibits an accretion outburst approximately once every year. Whether the thermal X-rays detected in intervening quiescent episodes are the result of cooling of the neutron star or due to continued low-level accretion remains unclear. In this work, we use Swift data obtained after the long and bright 2011 and 2013 outbursts, as well as the short and faint 2015 outburst, to investigate the hypothesis that cooling of the accretion-heated neutron star crust dominates the quiescent thermal emission in Aql X-1. We demonstrate that the X-ray light curves and measured neutron star surface temperatures are consistent with the expectations of the crust cooling paradigm. By using a thermal evolution code, we find that ? 1.2–3.2 MeV nucleon? 1 of shallow heat release describes the observational data well, depending on the assumed mass-accretion rate and temperature of the stellar core. We find no evidence for varying strengths of this shallow heating after different outbursts, but this could be due to limitations of the data. We argue that monitoring Aql X-1 for up to ? 1 yr after future outbursts can be a powerful tool to break model degeneracies and solve open questions about the magnitude, depth, and origin of shallow heating in neutron star crusts.
Serious games as innovative formative assessment tools for programming in Higher Education

Serious games are becoming increasingly popular as alternative supplementary learning approaches across all disciplines at all levels. Learners are more enabled to become more actively involved, not only in the learning process but also in the design and development of innovative formative assessment tools. This paper will present four serious games for programming education developed as part of a Serious Games honours year module in Higher Education at the University of the West of Scotland. Computer Games Development students were tasked as part of a research project to design and implement a serious game for students in their course or other Computer Science related courses in earlier years to provide their peers with innovative games for the purposes of formative assessment. It was hoped that the participants could enhance the engagement of courses that they had already passed but also utilise their creative Games Development skills in a new productive way to enhance the assessments in their own course having had the experience. Permitting students to design their own formative serious game assessments in this way enabled enhanced creativity with the students creatively tackling the overall problem in insightful and surprising ways. This paper will look at four games created for the purposes of teaching programming by analysing the overall learning outcomes, development process and providing a description of the games. The idea is to provide insight into the development process of serious games for programming education in terms of similarities, differences and to produce a basic framework for development in relation to content, assessment, and game mechanics. The paper will produce an overview of the excellent games created and present a case for increased active involvement of students to develop their own serious games – particularly on Computer Games degree or college courses.
A Formal Performance Evaluation Method for Customised Plug-and-Play Manufacturing Systems Using Coloured Petri Nets

Recent technological advancements and the evolution of industrial manufacturing paradigms have substantially increased the complexity of product-specific production systems. To reduce the time cost of modelling and verification and to enhance the degree of uniformity in the modelling process of system components, this article presents a componentised framework for domain modelling and performance analysis based on the concept of “multi-granularity and multi-view” for a production line of personalised and customised products, for plug-and-play manufacturing processes to involving a large number of model input parameters. The coloured Petri net tool is utilised as a simulation tool for mapping domain models to computational models for simulation and performance evaluation. This paper presents a method for setting the input parameters of a production system when using WIP, through-put and cycle time as metrics. The results of the performance analysis demonstrate the applicability of the proposed framework and provide direction for the production line’s layout design and scheduling strategy.
Deep Learning for Acoustic Irony Classification in Spontaneous Speech

Recognizing irony in speech and text can be challenging even for humans. For natural language processing (NLP) applications, irony recognition presents a unique challenge as irony alters the sentiment and meaning of the words themselves. Combining phonological insights from past literature on irony prosody and deep learning modeling, this research presents a new approach to irony classification in naturalistic speech data. A new corpus consisting of nearly five hours of irony-annotated, naturalistic, conversational speech data has been constructed for this study. A wide array of utterance-level and time-series acoustic features were extracted from this data and utilized in the training and fine-tuning of a series of deep learning approaches for irony classification. The best-performing model achieved an area under the curve of 0 . 811 in the speaker dependent condition, and 0 . 738 in the speaker independent condition, outperforming most irony classification models in the existing literature. In addition to the myriad real-world applications for this approach, its contribution to the understanding of prosodically-encoded augmentation of semantic content constitutes a significant step forward for research in the fields of linguistics and NLP.
MID-INFRARED SPECTRAL PROPERTIES OF POST-STARBURST QUASARS

We present Spitzer InfraRed Spectrograph low-resolution spectra of 16 spectroscopically selected post-starburst quasars (PSQs) at z ∼ 0.3. The optical spectra of these broad-lined active galactic nuclei (AGNs) simultaneously show spectral signatures of massive intermediate-aged stellar populations making them good candidates for studying the connections between AGNs and their hosts. The resulting spectra show relatively strong polycyclic aromatic hydrocarbon (PAH) emission features at 6.2 and 11.3 μm and a very weak silicate feature, indicative of ongoing star formation and low dust obscuration levels for the AGNs. We find that the mid-infrared composite spectrum of PSQs has spectral properties between ULIRGs and QSOs, suggesting that PSQs are hybrid AGN and starburst systems as also seen in their optical spectra. We also find that PSQs in early-type host galaxies tend to have relatively strong AGN activities, while those in spiral hosts have stronger PAH emission, indicating more star formation.
Protein prediction models support widespread post-transcriptional regulation of protein abundance by interacting partners

Protein and mRNA levels correlate only moderately. The availability of proteogenomics data sets with protein and transcript measurements from matching samples is providing new opportunities to assess the degree to which protein levels in a system can be predicted from mRNA information. Here we examined the contributions of input features in protein abundance prediction models. Using large proteogenomics data from 8 cancer types within the Clinical Proteomic Tumor Analysis Consortium (CPTAC) data set, we trained models to predict the abundance of over 13,000 proteins using matching transcriptome data from up to 958 tumor or normal adjacent tissue samples each, and compared predictive performances across algorithms, data set sizes, and input features. Over one-third of proteins (4,648) showed relatively poor predictability (elastic net r ≤ 0.3) from their cognate transcripts. Moreover, we found widespread occurrences where the abundance of a protein is considerably less well explained by its own cognate transcript level than that of one or more trans locus transcripts. The incorporation of additional trans-locus transcript abundance data as input features increasingly improved the ability to predict sample protein abundance. Transcripts that contribute to non-cognate protein abundance primarily involve those encoding known or predicted interaction partners of the protein of interest, including not only large multi-protein complexes as previously shown, but also small stable complexes in the proteome with only one or few stable interacting partners. Network analysis further shows a complex proteome-wide interdependency of protein abundance on the transcript levels of multiple interacting partners. The predictive model analysis here therefore supports that protein-protein interaction including in small protein complexes exert post-transcriptional influence on proteome compositions more broadly than previously recognized. Moreover, the results suggest mRNA and protein co-expression analysis may have utility for finding gene interactions and predicting expression changes in biological systems.
Opposite-sex associations are linked with annual fitness, but sociality is stable over lifetime

Animal sociality, an individual’s propensity to associate with others, has fitness consequences through mate choice, for example, directly, by increasing the pool of prospective partners, and indirectly through increased survival, and individuals benefit from both. Annually, fitness consequences are realised through increased mating success and subsequent fecundity. However, it remains unknown whether these consequences translate to life-time fitness. Here, we quantified social associations and their link to fitness annually and over lifetime, using a multi-generational, genetic pedigree. We used social network analysis to calculate variables representing different aspects of an individual’s sociality. Sociality showed high within-individual repeatability. We found that birds with more opposite-sex associates had higher annual fitness than those with fewer, but this did not translate to lifetime fitness. Instead, for lifetime fitness, we found evidence for stabilizing selection on opposite-sex sociality, and sociality in general, suggesting that reported benefits are only short-lived in a wild population, and that selection favours an average sociality.
IbpAB small heat shock proteins are not host factors for bacteriophage ϕX174 replication

Bacteriophages exploit host proteins for successful infection. Small heat shock proteins are a universally conserved family of stress-induced molecular chaperones that prevent irreversible aggregation of proteins. Two small heat shock proteins, IbpA and IbpB, are a class of holding modulators or “holdases”, which bind partially folded proteins and await ATP-driven folding chaperones for refolding. Bacteriophage ϕX174 is a small, icosahedral, and non-tailed virus belonging to the Microviridae. During ϕX174 infection of Escherichia coli C122, IbpA and IbpB were previously found to be the most highly upregulated host proteins, with expression levels comparable to ϕX174 proteins. In this work, to understand the role of IbpA and IbpB during ϕX174 infection, we used a hybrid approach of CRISPR interference and genomic knockouts to disrupt the ibpA and ibpB genes. We show that these two proteins do not appear to be necessary for efficient ϕX174 replication, and moreover, their absence has no effect on ϕX174 fecundity. Importance The small heat shock proteins (sHsps) are universally conserved family of stress-induced molecular chaperones that prevent irreversible protein aggregation. In E. coli, the IbpA/B sHsps work together, and separately, to bind partially folded proteins and await ATP-driven folding chaperones for refolding. These proteins are highly upregulated during protein overexpression and bacteriophage infection, but their collective role in bacteriophage infection has not been investigated. Here, we show that the ibpA/B genes are dispensable for bacteriophage ϕX174 infection, and are likely not essential host factors despite their abundance during diverse phage infections. Instead, this work points towards their role as cell wall integrity sensors, similar to the phage shock protein system, in addition to their canonical role as holdases of cytoplasmic protein.
Crossover from spin waves to diffusive spin excitations in underdoped Ba(Fe1-xCox)2As2

Using inelastic neutron scattering, we show that the onset of superconductivity in underdoped $\mathrm{Ba}({\mathrm{Fe}}_{1\ensuremath{-}x}{\mathrm{Co}}_{x}{)}_{2}{\mathrm{As}}_{2}$ coincides with a crossover from well-defined spin waves to overdamped and diffusive spin excitations. This crossover occurs despite the presence of long-range stripe antiferromagnetic order for samples in a compositional range from $x=0.04$ to 0.055, and is a consequence of the shrinking spin-density wave gap and a corresponding increase in the particle-hole (Landau) damping. The latter effect is captured by a simple itinerant model relating Co doping to changes in the hot spots of the Fermi surface. We argue that the overdamped spin fluctuations provide a pairing mechanism for superconductivity in these materials.
Bertrand mate of timelike biharmonic Legendre curves in Lorentzian Heisenberg group Heis3

Abstract In this paper, we study Bertrand mate of timelike biharmonic Legendre curves in the Lorentzian Heisenberg group Heis3. We characterize timelike biharmonic Legendre curves in terms of their curvature and torsion. Moreover, we obtain the position vectors of timelike biharmonic Legendre curves and we construct parametric equations of Bertrand mate of timelike biharmonic Legendre curves in the Lorentzian Heisenberg group Heis3.
Circadian desynchronization attenuates information throughput of prefrontal cortex pyramidal neurons in mice

The prefrontal cortex (PFC) is heavily involved in cognitive and emotional processes, including working memory, cognition, stress responses, and fear associated behaviors. Many PFC-associated behaviors are time-of-day dependent, and disruption of daily rhythms negatively impacts these behavioral outputs, yet how the disruption of daily rhythms impacts the fundamental function of PFC neurons, and the mechanism(s) by which this occurs, remains unknown. Using a mouse model, we demonstrate that the activity and action potential dynamics of prelimbic PFC neurons are regulated by time-of-day in a sex specific manner. Further, we show that postsynaptic K+ channels play a central role in mediating these rhythms, suggesting an intrinsic gating mechanism mediating information throughput. Finally, we demonstrate that environmental circadian desynchronization alters the intrinsic functioning of these neurons in part by increasing sensitivity GIRK channel activation. These key discoveries demonstrate daily rhythms contribute to the mechanisms underlying the essential physiology of PFC circuits, and provide potential mechanisms by which circadian disruption may impact the fundamental properties of neurons. Significance Statement Disruption of circadian rhythms, such as shift work and jet lag, are associated with negative physiological and behavioral outcomes, including changes in affective state, cognitive function, learning and memory. The prefrontal cortex (PFC) plays a critical role in these functions, yet how daily rhythms and desynchronization of these rhythms impact the physiology of neurons in the PFC is unknown. Here we demonstrate that daily rhythms impact the physiological function of PFC neurons in a sex-dependent manner, and that environmental circadian desynchronization alters PFC function irrespective of time-of-day. These findings provide not only a physiological context to the neural and behavioral changes associated with circadian desynchronization, but also highlight the importance of considering the temporal dimension in studies of neural circuits.
A resistance-gene-directed tolerance trait and selective inhibitors proffer HMG-CoA reductase as a new herbicide mode of action

Decades of intense herbicide use has led to resistance in weeds. Without innovative weed management practices and new herbicidal modes of action, the unabated rise of herbicide resistance will undoubtedly place further stress upon food security. HMGR (3-hydroxy-3-methylglutaryl-coenzyme A reductase) is the rate limiting enzyme of the eukaryotic mevalonate pathway successfully targeted by statins to treat hypercholesterolemia in humans. As HMGR inhibitors have been shown to be herbicidal, HMGR could represent a new mode of action target for the development of herbicides. Here we present the crystal structure of a HMGR from Arabidopsis thaliana (AtHMG1) which exhibits a wider active site than previously determined structures from different species. This plant conserved feature enabled the rational design of specific HMGR inhibitors, for which we engineered a tolerance trait through sequence analysis of fungal gene clusters. These results suggest HMGR to be a viable herbicide target modifiable to provide a tolerance trait.
Common neural choice signals emerge artifactually amidst multiple distinct value signals

A large body of work has identified characteristic neural signatures of value-based decision-making. A core circuit has been shown to track the values of options under consideration, and the dynamics of neural activity associated with this circuit have been found to closely resemble the ramping evidence accumulation process believed to underpin goal-directed choice, most notably in the centroparietal positivity (CPP). However, recent neuroimaging studies suggest that value-based choices trigger multiple value-related neural signatures, some of which are unrelated to decision-making per se but instead reflect reflexive affective reactions to one’s options. Here, we use the temporal resolution of EEG to test whether choice-independent value signals could be dissociated from well-known temporal signatures of the choice process. We show that EEG activity during value-based choice can be decomposed into distinct spatiotemporal clusters, one stimulus-locked (associated with the affective salience of a choice set) and one response-locked (associated with the difficulty of selecting the best option). We show that neither of these clusters meet the criteria for an evidence accumulation signal. Instead, and to our surprise, we find across two studies that stimulus-locked activity can mimic an evidence accumulation process when aligned to the response (as with the CPP). We then re-analyze four previous studies that demonstrate a response-locked evidence accumulation signal in the CPP – one during value-based decision-making, the others during perceptual decision-making – and show that this signal disappears when stimulus-locked and response-locked signals are jointly accounted for. Collectively, our findings show that neural signatures of value can reflect choice-independent processes that when analyzed using standard approaches, can look deceptively like evidence accumulation. Significance Statement To choose, people must evaluate their options and select between them. Selection is well described by a process of accumulating evidence up to some threshold, with an electrophysiological signature in the centroparietal positivity (CPP). However, decision-making also gives rise to value signals reflecting affective reactions and other selection-unrelated processes. Measuring EEG while participants made value-based choices, we identified two spatiotemporally distinct value signals, neither reflecting evidence accumulation. Instead, we show that evidence accumulation signals found in the CPP can arise artifactually from overlapping stimulus- and response-related activity. These findings call for a significant reexamination of established links between neural and computational mechanisms of choice, while inviting deeper consideration of the array of cognitive and affective processes that occur in parallel.