Miracle-dz/UniFAR-FTUs huggingface dataset:
Uncertainty-wise Requirements Prioritization with Search

Requirements review is an effective technique to ensure the quality of requirements in practice, especially in safety-critical domains (e.g., avionics systems, automotive systems). In such contexts, a typical requirements review process often prioritizes requirements, due to limited time and monetary budget, by, for instance, prioritizing requirements with higher implementation cost earlier in the review process. However, such a requirement implementation cost is typically estimated by stakeholders who often lack knowledge about (future) requirements implementation scenarios, which leads to uncertainty in cost overrun. In this article, we explicitly consider such uncertainty (quantified as cost overrun probability) when prioritizing requirements based on the assumption that a requirement with higher importance, a higher number of dependencies to other requirements, and higher implementation cost will be reviewed with the higher priority. Motivated by this, we formulate four objectives for uncertainty-wise requirements prioritization: maximizing the importance of requirements, requirements dependencies, the implementation cost of requirements, and cost overrun probability. These four objectives are integrated as part of our search-based uncertainty-wise requirements prioritization approach with tool support, named as URP. We evaluated six Multi-Objective Search Algorithms (MOSAs) (i.e., NSGA-II, NSGA-III, MOCell, SPEA2, IBEA, and PAES) together with Random Search (RS) using three real-world datasets (i.e., the RALIC, Word, and ReleasePlanner datasets) and 19 synthetic optimization problems. Results show that all the selected MOSAs can solve the requirements prioritization problem with significantly better performance than RS. Among them, IBEA was over 40% better than RS in terms of permutation effectiveness for the first 10% of prioritized requirements in the prioritization sequence of all three datasets. In addition, IBEA achieved the best performance in terms of the convergence of solutions, and NSGA-III performed the best when considering both the convergence and diversity of nondominated solutions.
A Brief Comment on Indirect Methods for Measuring Unsaturated Hydraulic Conductivity

Because of the complicated structure of unsaturated soil, direct measurement of unsaturated hydraulic conductivity in the laboratory is a very difficult process. Therefore, the indirect methods for measuring unsaturated hydraulic conductivity are widely used in practice. This paper mainly introduces the development of indirect methods, moreover, analyzes and compares the advantages and disadvantages of them briefly .
Ultrafast nanoimaging of the order parameter in a structural phase transition

Watching a phase transition unfold The layered material 1 T-polytype of tantalum disulfide has several intricate charge-ordered phases. How exactly one phase transitions into another is tricky to observe directly with current technologies. Danz et al. used pump-probe ultrafast dark-field electron microscopy to follow such a transition with fine spatial and temporal resolution (see the Perspective by Kogar). To achieve that goal, they shaped the electron beam used as the probe to bring out the features peculiar to the transition. Science, this issue p. 371; see also p. 341 Ultrafast, spatially resolved dark-field electron microscopy is used to monitor a transition between the phases of 1T-TaS2. Understanding microscopic processes in materials and devices that can be switched by light requires experimental access to dynamics on nanometer length and femtosecond time scales. Here, we introduce ultrafast dark-field electron microscopy to map the order parameter across a structural phase transition. We use ultrashort laser pulses to locally excite a 1T-TaS2 (1T-polytype of tantalum disulfide) thin film and image the transient state of the specimen by ultrashort electron pulses. A tailored dark-field aperture array allows us to track the evolution of charge-density wave domains in the material with simultaneous femtosecond temporal and 5-nanometer spatial resolution, elucidating relaxation pathways and domain wall dynamics. The distinctive benefits of selective contrast enhancement will inspire future beam-shaping technology in ultrafast transmission electron microscopy.
Study of Fabry-Perot Etalon Stability and Tuning for Spectroscopic Rayleigh Scattering

[Abstract] The Fabry-Perot interferometer is a commonly employed instrument for resolving the spectrum of molecular Rayleigh scattered light for the purpose of evaluating flow properties such as gas velocity and temperature. Rayleigh scattered light from a focused laser beam can be directly imaged through a solid Fabry-Perot etalon onto a CCD detector to provide the spectral content of the scattered light. The spatial resolution of the measurements is governed by the locations of interference fringes. The location of the fringes can be changed by altering the etalon’s physical characteristics, such as thickness and index of refraction. For a fused silica solid etalon the physical properties can be adjusted by changing the etalon temperature; hence changing the order of the interference pattern and the physical fringe locations. Controlling the temperature of the etalon can provide for a slow time-response spatial scanning method for this type of etalon system. A custom designed liquid crystal Fabry-Perot (LCFP) can provide for a fast time-response method of scanning the etalon system. Voltage applied to the liquid crystal interface sets the etalon’s properties allowing Rayleigh measurements to be acquired at varying spatial locations across the image of the laser beam over a very short time period. A standard fused silica etalon and a tunable LCFP etalon are characterized to select the system that is best suited for Rayleigh scattering measurements in subsonic and supersonic flow regimes. A frequency-stabilized laser is used to investigate the apparent frequency stability and temperature sensitivity of the etalon systems. Frequency stability and temperature sensitivity data of the fused silica and LCFP etalon systems are presented in this paper, along with measurements of the LCFP etalon’s tuning capabilities. Rayleigh scattering velocity measurements with both etalon systems are presented, in an effort to determine which etalon is better suited to provide optical flow measurements of velocity, temperature, and density.
Complete Genome Sequence of Klebsiella pneumoniae Myophage Muenster

Klebsiella pneumoniae is associated with antibiotic-resistant nosocomial infections. Here, we present the annotated genome sequence of the Klebsiella jumbo phage Muenster. The Muenster genome sequence (346,937 bp) encodes 6 tRNAs and 561 putative protein-coding genes, including 9 tail fibers, suggesting a genetic mechanism to broaden the host range. ABSTRACT Klebsiella pneumoniae is associated with antibiotic-resistant nosocomial infections. Here, we present the annotated genome sequence of the Klebsiella jumbo phage Muenster. The Muenster genome sequence (346,937 bp) encodes 6 tRNAs and 561 putative protein-coding genes, including 9 tail fibers, suggesting a genetic mechanism to broaden the host range.
Prosodic categories in speech are acoustically multidimensional: evidence from dimension-based statistical learning

| Segmental speech units (e.g. phonemes) are described as multidimensional categories wherein perception involves contributions from multiple acoustic input dimensions, and the relative perceptual weights of these dimensions respond dynamically to context. Can prosodic aspects of speech spanning multiple phonemes, syllables or words be characterized similarly? Here we investigated the relative contribution of two acoustic dimensions to word emphasis. Participants categorized instances of a two-word phrase pronounced with typical covariation of fundamental frequency (F0) and duration, and in the context of an artificial ‘accent’ in which F0 and duration covaried atypically. When categorizing ‘accented’ speech, listeners rapidly downweighted the secondary dimension (duration) while continuing to rely on the primary dimension (F0). This clarifies two core theoretical questions: 1) prosodic categories are signalled by multiple input acoustic dimensions and 2) perceptual cue weights for prosodic categories dynamically adapt to local regularities of speech input.
Evolution of cytokine production capacity in ancient and modern European populations

As our ancestors migrated throughout the different continents, natural selection increased the presence of alleles advantageous in the new environments. Heritable variations that alter the susceptibility to diseases vary with the historical period, the virulence of the infections, and their geographical spread. In this study we built polygenic scores for heritable traits influencing the genetic adaptation in the production of cytokines and immune-mediated disorders, including infectious, inflammatory, and autoimmune diseases, and applied them to the genomes of several ancient European populations. We observed that the advent of the Neolithic was a turning point for immune-mediated traits in Europeans, favoring those alleles linked with the development of tolerance against intracellular pathogens and promoting inflammatory responses against extracellular microbes. These evolutionary patterns are also associated with an increased presence of traits related to inflammatory and auto-immune diseases.
Adiponectin preserves metabolic fitness during aging

Adiponectin is essential for the regulation of tissue substrate utilization and systemic insulin sensitivity. Clinical studies have suggested a positive association of circulating adiponectin with healthspan and lifespan. However, the direct effects of adiponectin on promoting healthspan and lifespan remain unexplored. Here, we are using an adiponectin null mouse and a transgenic adiponectin overexpression model. We directly assessed the effects of circulating adiponectin on the aging process and found that adiponectin null mice display exacerbated age-related glucose and lipid metabolism disorders. Moreover, adiponectin null mice have a significantly shortened lifespan on both chow and high-fat diet (HFD). In contrast, a transgenic mouse model with elevated circulating adiponectin levels has a dramatically improved systemic insulin sensitivity, reduced age-related tissue inflammation and fibrosis, and a prolonged healthspan and median lifespan. These results support a role of adiponectin as an essential regulator for healthspan and lifespan.
RIPK3 promoter hypermethylation in hepatocytes protects from bile acid induced inflammation and necroptosis

Background & Aims Necroptosis facilitates cell death in a controlled manner and is employed by many cell types following injury. It plays a major role in various liver diseases, albeit the cell type-specific regulation of necroptosis in the liver and especially hepatocytes has not yet been conceptualized. Approaches & Results Here, we demonstrate that DNA methylation suppresses RIPK3 expression in human hepatocytes and HepG2 cells. In diseases leading to cholestasis the RIPK3 expression is induced in mice and humans in a cell-type specific manner. Over-expression of RIPK3 in HepG2 cells leads immediately to RIPK3 activation by phosphorylation that is further modulated by different bile acids. Conclusion Bile acids mediated RIPK3 activation facilitates the secretion and expression of IL-8 via the JNK-pathway, suggesting hepatocytes suppress RIPK3 expression to protect themselves from bile acid induced necroptosis and inflammation but in chronical liver diseases associated with cholestasis induction of RIPK3 expression may be an early event signaling danger and repair through release of IL-8. Graphical abstract
Predicting lifestyle and host from positive selection data and genome properties in oomycetes

Background Host and niche shifts are a source of genomic and phenotypic diversification as evidenced in parasitism. Exemplary is core metabolism reduction as parasites adapt to a particular host, while the accessory genome often maintains a high degree of diversification. However, selective pressures acting on the genome of organisms that have undergone lifestyle or host change have not been fully investigated. Results Here, we developed a comparative genomics approach to study underlying adaptive trends in oomycetes, a eukaryotic phylum with a broad range of economically important plant and animal parasitic lifestyles. Our analysis reveals converging evolution on biological processes for oomycetes that have similar lifestyle. Besides, we find that certain functions, in particular carbohydrate metabolism, transport, and signaling, are important for host and environmental adaption in oomycetes. Discussion Given the high correlation between lifestyle and genome properties in our oomycete dataset and the convergent evolution of fungal and oomycete genomes, we have developed a model that predicts plant pathogen lifestyles with high accuracy based on functional annotations. Understanding how genomes and selective pressures correlate with lifestyle may be crucial to identify new emerging diseases and pandemic threats.
Serotonin modulates learning content-specific neuroplasticity of functional brain networks

Learning-induced neuroplastic changes, further modulated by content and setting, are mirrored in brain functional connectivity (FC). In animal models, serotonergic agents were shown to facilitate neuroplasticity. This is especially prominent during emotional relearning, such as fear extinction, which may translate to clinical improvements in human patients. To investigate this assumption, 99 healthy subjects underwent six weeks of emotional or non-emotional learning and subsequent relearning. Resting-state functional magnetic resonance imaging was performed before and after the learning phases to investigate changes in FC. During relearning, subjects received either a daily dose of the selective serotonin reuptake inhibitor (SSRI) escitalopram or placebo. Escitalopram intake modulated FC changes in a network comprising Broca’s area, the medial prefrontal cortex, the right inferior temporal and left lingual gyrus. More specifically, escitalopram increased the bidirectional connectivity between medial prefrontal cortex and lingual gyrus for non-emotional and additionally the connectivity from medial prefrontal cortex to Broca’s area for emotional relearning. The context-dependence of these effects supports the assumption that SSRIs in clinical practice might improve neuroplasticity rather than psychiatric symptoms per se. Correlations with learning behavior further point towards a relationship with extinction processes in relearning. These results demonstrate that escitalopram intake during relearning results in content-dependent network adaptations and support the conclusion that enhanced neuroplasticity might be the major underlying mechanism also in humans. Beyond expanding the complexities of learning, these findings emphasize the influence of external factors on serotonin-facilitated neuroplasticity of the human brain.
Graded Visual Consciousness During the Attentional Blink

One of the ongoing debates about visual consciousness is whether it can be considered as an all-or-none or a graded phenomenon. This may depend on the experimental paradigm and the task used to investigate this question. The present event-related potential study (N = 32) focuses on the attentional blink paradigm for which so far only little and mixed evidence is available. Detection of T2 face targets during the attentional blink was assessed via an objective accuracy measure (reporting the faces’ gender), subjective visibility on a perceptual awareness scale (PAS) as well as event-related potentials time-locked to T2 onset (components P1, N1, N2, and P3). The behavioral results indicate a graded rather than an all-or-none pattern of visual awareness. Corresponding graded differences in the N1, N2, and P3 components were observed for the comparison of visibility levels. These findings suggest that conscious perception during the attentional blink can occur in a graded fashion.
Single-cell analysis of colonic epithelium reveals unexpected shifts in cellular composition and molecular phenotype in treatment-naïve adult Crohn’s disease

The intestinal epithelial barrier is comprised of a monolayer of specialized intestinal epithelial cells (IECs) that are critical in maintaining gut mucosal homeostasis. Dysfunction within various IEC fractions can increase intestinal permeability, resulting in a chronic and debilitating condition known as Crohn’s disease (CD). Defining the molecular changes in each IEC type in CD will contribute to an improved understanding of the pathogenic processes and the identification of potential therapeutic targets. Here we performed, for the first time at single-cell resolution, a direct comparison of the colonic epithelial cellular and molecular landscape between treatment-naïve adult CD and non-IBD control patients. Our analysis revealed that in CD patients there is a significant skew in the colonic epithelial cellular distribution away from canonical LGR5+ stem cells, located at the crypt-bottom, and toward one specific subtype of mature colonocytes, located at the crypt-top. Further analysis revealed unique changes to gene expression programs in every major cell type, including a previously undescribed suppression in CD of most enteroendocrine driver genes as well as L-cell markers including GCG. We also dissect a previously poorly understood SPIB+ cell cluster, revealing at least four sub-clusters that exhibit unique features. One of these SPIB+ sub-clusters expresses crypt-top colonocyte markers and is significantly up-regulated in CD, whereas another sub-cluster strongly expresses and stains positive for lysozyme (albeit no other canonical Paneth cell marker), which surprisingly is greatly reduced in expression in CD. Finally, through integration with data from genome-wide association studies, we show that genes implicated in CD risk exhibit heretofore unknown cell-type specific patterns of aberrant expression in CD, providing unprecedented insight into the potential biological functions of these genes.
Single Cell Label-Free Probing of Chromatin Dynamics During B Lymphocyte Maturation

Large-scale intracellular signalling during developmental growth or in response to environmental alterations are largely orchestrated by chromatin within the cell nuclei. Chemical and conformational modifications of the chromatin architecture are critical steps in the regulation of differential gene expression and ultimately cell fate determination. Therefore, establishing chemical properties of the nucleus could provide key markers for phenotypic characterisation of cellular processes on a scale of individual cells. Raman microscopy is a sensitive technique that is capable of probing single cell chemical composition - and sub-cellular regions - in a label-free optical manner. As such, it has great potential in both clinical and basic research. However, perceived limitations of Raman spectroscopy such as low signal intensity and the difficulty in linking alterations in vibrational signals directly with ensuing biological effects have hampered advances in the field. Here we use immune B lymphocyte development as a model to assess chromatin and transcriptional changes using confocal Raman microscopy in combination with microfluidic devices and correlative transcriptomics, thereby linking changes in chemical and structural properties to biological outcomes. Live B lymphocytes were assessed before and after maturation. Multivariate analysis was applied to distinguish cellular components within each cell. The spectral differences between non-activated and activated B lymphocytes were then identified, and their correlation with known intracellular biological changes were assessed in comparison to conventional RNA-seq analysis. Our data shows that spectral analysis provides a powerful tool to study gene activation that can complement conventional molecular biology techniques and opens the way for mapping the dynamics in the biochemical makeup of individual cells.
An open-source tool to assess the carbon footprint of research

The scrutiny over the carbon footprint of research and higher education has increased rapidly in the last few years. This has resulted in a series of publications providing various estimates of the carbon footprint of one or several research activities, principally at the scale of a university or a research center or, more recently, a field of research. The variety of tools or methodologies on which these estimates rely unfortunately prevents any aggregation or direct comparison. This is because carbon footprint assessments are very sensitive to key parameters (e.g., emission factors) or hypotheses (e.g., scopes). Hence, it is impossible to address fundamental questions such as: is the carbon footprint of research structurally different between disciplines? Are plane trips a major source of carbon emissions in academic research? Massive collection and curation of carbon footprint data, across a large array of research situations and disciplines, is hence an important, timely and necessary challenge to answer these questions. This paper presents a framework to collect and analyse large amounts of homogeneous research carbon emission data in a network of research entities at the national scale. It relies on an open-source web application, GES 1point5, designed to estimate the carbon footprint of a department, research lab or team in any country of the world. Importantly, GES 1point5 is also designed to aggregate all input data and corresponding GHG emissions estimates into a comprehensive database. GES 1point5 therefore enables (i) the identification of robust local or national determinants of the carbon footprint of research and (ii) the estimation of the carbon footprint of the entire research sector at national scale. A preliminary analysis of the carbon footprint of more than one hundred laboratories in France is presented to illustrate the potential of the framework. It shows that the average emissions are 479 t CO2e for a research lab and 3.6 t CO2e for an average lab member (respectively 404 and 3.1 t CO2e without accounting for the indirect radiative effects of aviation), with the current scope of GES 1point5. Availability and implementation: GES 1point5 is available online at http://labos1point5.org/ges- 1point5 and its source code can be downloaded from the GitLab platform at https://framagit.org/ labos1point5/l1p5-vuejs.
Cavin4 interacts with Bin1 to promote T-tubule formation and stability in developing skeletal muscle

The cavin proteins are essential for caveola biogenesis and function. Here, we identify a role for the muscle-specific component, Cavin4, in skeletal muscle T-tubule development by analyzing two vertebrate systems: mouse and zebrafish. In both models Cavin4 localized to T-tubules and loss of Cavin4 resulted in aberrant T-tubule maturation. In zebrafish, which possess duplicated cavin4 paralogs, Cavin4b was shown to directly interact with the T-tubule-associated BAR domain protein, Bin1. Loss of both Cavin4a and Cavin4b caused aberrant accumulation of interconnected caveolae within the T-tubules, a fragmented T-tubule network enriched in Caveolin-3, and an impaired Ca2+ response upon mechanical stimulation. We propose a role for Cavin4 in remodeling the T-tubule membrane early in development by recycling caveolar components from the T-tubule to the sarcolemma. This generates a stable T-tubule domain lacking caveolae that is essential for T-tubule function.