Miracle-dz/UniFAR-FTUs huggingface dataset:
Aero-Propulsive Model Design from a Commercial Aircraft in Climb and Cruise Regime using Performance Data =

IATA has estimated, in 2012, at about 2% of global carbon dioxide emissions, the environmental impact of the air transport, as a consequence caused by the rapidly growing of global movement demand of people and goods, and which was effectively taken into account in the development of the aviation industry. The historic achievements of scientific and technical progress in the field of commercial aviation were contributed to this estimate, and even today the research continues to make progress to help to reduce the emissions of greenhouse gases. Advances in commercial aircraft, and its engine design technology had the aim to improve flight performance. These improvements have enhanced the global flight planning of these types of aircrafts. Almost all of these advances rely on generated performance data as reference sources, the most of which are classified as “confidential” by the aircraft manufacturers. There are very few aero-propulsive models conceived for the climb regime in the literature, but none of them was designed without access to an engine database, and/or to performance data in climb and in cruise regimes with direct applicability for flight optimization. In this thesis, aero-propulsive models methodologies are proposed for climb and cruise regimes, using system identification and validation methods, through which airplane performance can be computed and stored in the most compact and easily accessible format for this kind of performance data. The acquiring of performance data in this format makes it possible to optimize flight profiles, used by on-board Flight Management Systems. The aero-propulsive models developed here were investigated on two aircrafts belonging to commercial class, and both of them had offered very good accuracy. One of their advantages is that they can be adapted to any other aircraft of the same class, even if there is no access to their corresponding engine flight data. In addition, these models could save airlines a considerable amount of money, given the fact that the number of flight tests could be drastically reduced. Lastly, academia, thus the laboratory of applied research in active control, avionics and aeroservoelasticity (LARCASE) team is gaining direct access to these aircraft performance data to obtain experience in novel optimization algorithms of flight profiles.
A Debugging Game for Probabilistic Models

One of the major advantages of model checking over other formal methods is its ability to generate a counterexample when a model does not satisfy is its specification. A counterexample is an error trace that helps to locate the source of the error. Therefore, the counterexample represents a valuable tool for debugging. In Probabilistic Model Checking (PMC), the task of counterexample generation has a quantitative aspect. Unlike the previous methods proposed for conventional model checking that generate the counterexample as a single path ending with a bad state representing the failure, the task in PMC is completely different. A counterexample in PMC is a set of evidences or diagnostic paths that satisfy a path formula, whose probability mass violates the probability threshold. Counterexample generation is not sufficient for finding the exact source of the error. Therefore, in conventional model checking, many debugging techniques have been proposed to act on the counterexamples generated to locate the source of the error. In PMC, debugging counterexamples is more challenging, since the probabilistic counterexample consists of multiple paths and it is probabilistic. In this article, we propose a debugging technique based on stochastic games to analyze probabilistic counterexamples generated for probabilistic models described as Markov chains in PRISM language. The technique is based mainly on the idea of considering the modules composing the system as players of a reachability game, whose actions contribute to the evolution of the game. Through many case studies, we will show that our technique is very effective for systems employing multiple components. The results are also validated by introducing a debugging tool called GEPCX (Game Explainer of Probabilistic Counterexamples).
FuzzyData: A Scalable Workload Generator for Testing Dataframe Workflow Systems

Dataframes have become a popular means to represent, transform and analyze data. This approach has gained traction and a large user base for data science practitioners - resulting in a new wave of systems that implement a dataframe API but allow for performance, efficiency, and distributed/parallel extensions to systems such as R and pandas. However, unlike relational databases and NoSQL systems with a variety of benchmarking, testing, and workload generation suites, there is an acute lack of similar tools for dataframe-based systems. This paper presents fuzzydata, a first step in providing an extensible workflow generation system that targets dataframe-based APIs. We present an abstract data processing workflow model, random table and workflow generators, and three clients implemented using our model. Using fuzzydata, we can encode a real-world workflow or randomly generate workflows using various parameters. These workflows can be scaled and replayed on multiple systems to provide stress testing, performance evaluation, and a breakdown of performance bottlenecks present on popular dataframe systems.
Highly Parallel Multi-FPGA System Compilation from Sequential C/C++ Code in the AWS Cloud

We present a High Level Synthesis compiler that automatically obtains a multi-chip accelerator system from a single-threaded sequential C/C++ application. Invoking the multi-chip accelerator is functionally identical to invoking the single-threaded sequential code the multi-chip accelerator is compiled from. Therefore, software development for using the multi-chip accelerator hardware is simplified, but the multi-chip accelerator can exhibit extremely high parallelism. We have implemented, tested, and verified our push-button system design model on multiple field-programmable gate arrays (FPGAs) of the Amazon Web Services EC2 F1 instances platform, using, as an example, a sequential-natured DES key search application that does not have any DOALL loops and that tries each candidate key in order and stops as soon as a correct key is found. An 8- FPGA accelerator produced by our compiler achieves 44,600 times better performance than an x86 Xeon CPU executing the sequential single-threaded C program the accelerator was compiled from. New features of our compiler system include: an ability to parallelize outer loops with loop-carried control dependences, an ability to pipeline an outer loop without fully unrolling its inner loops, and fully automated deployment, execution and termination of multi-FPGA application-specific accelerators in the AWS cloud, without requiring any manual steps.
Chinese Event Extraction via Graph Attention Network

Event extraction plays an important role in natural language processing (NLP) applications, including question answering and information retrieval. Most of the previous state-of-the-art methods were lack of ability in capturing features in long range. Recent methods applied dependency tree via dependency-bridge and attention-based graph. However, most of the automatic processing tools used in those methods show poor performance on Chinese texts due to mismatching between word segmentation and labels, which results in error propagation. In this article, we propose a novel character-level Chinese event extraction framework via graph attention network (CAEE). We build our model upon the sequence labeling model, but enhance it with word information by incorporating the word lexicon into the character representations. We further exploit the inter-dependencies between event triggers and argument by building a word-character-based graph network via syntactic shortcut arcs with dependency-parsing. The architecture of the graph minimizes error propagation, which is the result of the error detection of the word boundaries in the processing of Chinese texts. To demonstrate the effectiveness of our work, we build a large-scale real-world corpus consisting of announcements of Chinese financial news without golden entities. Experiments on the corpus show that our approach achieves competitive results compared with previous work in the field of Chinese texts.
Structural basis underlying specific biochemical activities of non-muscle tropomyosin isoforms

The actin cytoskeleton is critical for cell migration, morphogenesis, endocytosis, organelle dynamics, and cytokinesis. To support diverse cellular processes, actin filaments form a variety of structures with specific architectures and dynamic properties. Key proteins specifying actin filaments are tropomyosins. Non-muscle cells express several functionally non-redundant tropomyosin isoforms, which differentially control the interactions of other proteins, including myosins and ADF/cofilin, with actin filaments. However, the underlying molecular mechanisms have remained elusive. By determining the cryogenic electron microscopy structures of actin filaments decorated by two functionally distinct non-muscle tropomyosin isoforms, Tpm1.6 and Tpm3.2, we reveal that actin filament conformation remains unaffected upon binding. However, Tpm1.6 and Tpm3.2 follow different paths along the major groove of the actin filament, providing an explanation for their incapability to co-polymerize on actin filaments. The structures and biochemical work also elucidate the molecular basis underlying specific roles of Tpm1.6 and Tpm3.2 in myosin II activation and protecting actin filaments from ADF/cofilin-catalysed severing.
A Multimodal Neuroimaging Dataset to Study Spatiotemporal Dynamics of Visual Processing in Humans

We describe structural and multimodal functional neuroimaging data collected from 21 healthy volunteers. Functional magnetic resonance images (fMRI) and electroencephalography (EEG) signals were acquired in separate sessions from the same individuals while they were performing a visual one-back repetition task. During functional sessions, participants were presented with images from five categories, including animals, chairs, faces, fruits, and vehicles. The stimulus set and experimental parameters were chosen to be similar to that of an available electrocorticography (ECoG) dataset, therefore creating a unique opportunity to study vision in humans with multiple complementary neuroimaging modalities. Individual-specific head models can be constructed for each participant using T1-weighted MPRAGE images and the recorded positions of the EEG electrodes. By combining the three functional modalities and the structural data, this dataset provides a unique setting to explore spatiotemporal dynamics of invariant object recognition in humans. This multimodal data can also be used to develop new methods for combining fMRI and electrophysiological modalities to come up with more accurate spatiotemporally resolved maps of brain function, which is inaccessible by any of the modalities alone.
Ancient DNA from the extinct New Zealand grayling (Prototroctes oxyrhynchus) reveals evidence for Miocene marine dispersal

The evolutionary history of Southern Hemisphere graylings (Retropinnidae) in Aotearoa New Zealand—including the number of colonisation events, the directionality and timing of dispersal, and their relationship to the Australian grayling—is poorly understood. The New Zealand grayling (Prototroctes oxyrhynchus) is the only known freshwater fish species to have gone extinct since human arrival in New Zealand. Despite its historical abundance, only 23 formalin-fixed specimens (both wet and dried) exist in museum collections globally, which were previously non-amenable to palaeogenetic analysis. Here, we used high-throughput DNA sequencing techniques, specifically designed for formalin-fixed specimens, to generate mitochondrial genomes of P. oxyrhynchus, and analysed these within a temporal phylogenetic framework of retropinnid and osmerid taxa. We recovered strong evidence for a sister relationship between the New Zealand and Australian grayling (P. mareana), with the two having a common ancestor around 13.8 Mya (95% HPD: 6.1–23.2 Mya), after the height of Oligocene marine inundation in New Zealand. Our temporal phylogenetic analysis suggests a single marine dispersal event between New Zealand and Australia, though the direction of dispersal is equivocal, followed by divergence into genetically and morphologically distinguishable species through isolation by distance. This study provides further insights into the possible drivers of the extinction of the New Zealand grayling, and highlights how advancements in palaeogenetic techniques can be used to test evolutionary hypotheses in extinct (and living) fish, which have been comparatively neglected in the field of ancient DNA.
Vitamin K-dependent carboxylation regulates Ca2+ flux and adaptation to metabolic stress in β cells

Vitamin K is a micronutrient necessary for the γ-carboxylation of glutamic acids. This post-translational modification occurs in the endoplasmic reticulum (ER) and affects secreted proteins. Clinical studies have recently implicated vitamin K in the pathophysiology of diabetes, but the underlying molecular mechanism remains unknown. Here, we show that mouse β-cells lacking γ-carboxylation fail to adapt their insulin secretion in the context of age-related insulin resistance or diet-induced β-cell stress. In human islets, γ-carboxylase expression positively correlates with improved insulin secretion in response to glucose. We identified Endoplasmic Reticulum Gla Protein (ERGP) as a novel γ-carboxylated ER-resident calcium-binding protein expressed in β-cells. Mechanistically, γ-carboxylation of ERGP protects cells against calcium overfilling by diminishing STIM1 and Orai1 interaction and restraining store-operated calcium entry. These results reveal a critical role for vitamin K-dependent γ-carboxylation in the regulation of calcium flux in β-cells and in their capacity to adapt to metabolic stress.
Sleep does not influence schema-facilitated motor memory consolidation

Study Objectives Novel information is rapidly learned when it is compatible with previous knowledge. This “schema” effect, initially described for declarative memories, was recently extended to the motor memory domain. Importantly, this beneficial effect was only observed 24 hours – but not immediately – following motor schema acquisition. Given the established role of sleep in memory consolidation, we hypothesized that sleep following the initial learning of a schema is necessary for the subsequent rapid integration of novel motor information. Methods Two experiments were conducted to investigate the effect of diurnal and nocturnal sleep on schema-mediated motor sequence memory consolidation. In Experiment 1, participants first learned an 8-element motor sequence through repeated practice (Session 1). They were then afforded a 90-minute nap opportunity (N=25) or remained awake (N=25) before learning a second motor sequence (Session 2) which was highly compatible with that learned prior to the sleep/wake interval. Experiment 2 was similar; however, Sessions 1 and 2 were separated by a 12-hour interval that included nocturnal sleep (N=28) or only wakefulness (N=29). Results For both experiments, we found no group differences in motor sequence performance (reaction time and accuracy) following the sleep/wake interval. Furthermore, in Experiment 1, we found no correlation between sleep features (non-REM sleep duration, spindle and slow wave activity) and post-sleep behavioral performance. Conclusions The results of this research suggest that integration of novel motor information into a cognitive-motor schema does not specifically benefit from post-learning sleep.
MYC Overexpression Drives Immune Evasion in Human Cancer that is Reversible Through Restoration of Pro-Inflammatory Macrophages

Cancers evade immune surveillance that in some, but not in many, cases can be reversed through immune checkpoint therapy. Here we report that the MYC oncogene suppresses immune surveillance, activates immune checkpoint expression, and predicts responsiveness to immune checkpoint inhibition. First, when MYC is genomically amplified and overexpressed in 33 different human cancers, this increases immune checkpoint expression, drives immune checkpoint therapeutic resistance, and is associated with both Th2-like immune profile, and reduced CD8 T cell infiltration. Second, experimentally, MYC-driven tumors suppress pro-inflammatory antigen-presenting macrophages with increased CD40 and MHCII expression, which in turn impedes T cell response. This MYC-driven suppression of macrophages can be reversed by combined but not individual blockade of PDL1 and CTLA4. Third, the depletion of macrophages abrogated the anti-neoplastic effects of PDL1 and CTLA4 blockade. Hence, MYC is a predictor of immune checkpoint responsiveness and a key driver of immune evasion through the suppression of pro-inflammatory macrophages. The immune evasion by MYC can be overcome by combined PDL1 and CTLA4 blockade. Statement of Significance MYC is the most commonly activated oncogene in human cancers. In this study, we identify macrophage-mediated immune evasion as a major therapeutic vulnerability of MYC-driven cancers. Our results have implications for developing effective immunotherapies for MYC-driven human cancers and also for prioritizing patients with MYC-driven tumors for combination immunotherapy.
Application and comparison of lyophilisation protocols to enhance stable long-term storage of filovirus pseudotypes for use in antibody neutralisation tests

Filoviruses encompass highly pathogenic viruses placing sporadic public health burden on countries affected. Efforts for improved diagnostics and surveillance are needed considering the recent Ebola outbreaks in Africa. The need for high containment facilities can be circumvented by the use of pseudotype viruses (PV), which can be handled in low containment, for tropism, drug screening, vaccine immunogenicity and serosurveillance studies. In this study we assessed stability and functionality after long-term storage of lyophilised filovirus pseudotypes for use in neutralisation assays. Lyophilised Ebola and Marburg PVs retained production titres for at least two years when stored at +4°C or less. Lyophilised Ebola PVs performed similarly to non-lyophilised PVs in neutralisation assays after reconstitution. When stored at high temperatures (+37°C), lyophilised PVs did not retain titres after one-month storage, however, when lyophilised using pilot scale facilities EBOV PVs retained titres and performed well in neutralisation assays after one-month storage at 37°C suggesting removing residual moisture might be crucial for avoiding cold-chain transportation. Lyophilisation could allow reagents to be transported more efficiently as well as reducing costs for a future serological kit.
Arf GTPase activates the WAVE Regulatory Complex through a novel binding site

Crosstalk between Rho- and Arf-family GTPases plays an important role in linking actin cytoskeletal remodeling to membrane protrusion, organelle structure, and vesicle trafficking. The central actin regulator, WAVE Regulatory Complex (WRC), is a converging point of Rac1 (a Rho-family GTPase) and Arf signaling in many processes, but how Arf promotes WRC activation is unknown. Here we reconstituted a direct interaction between Arf and WRC. This interaction can be greatly enhanced by Rac1 binding to the D site of the WRC. Arf1 binds to a newly identified conserved surface on Sra1 located between the D site and the WH2 helix of WAVE1, which can drive WRC activation using a mechanism distinct from that of Rac1. Mutating Arf binding site abolishes Arf1-WRC interaction, disrupts Arf1-mediated WRC activation, and impairs lamellipodia morphology. This work uncovers a new mechanism underlying WRC activation and provides a mechanistic foundation for studying how WRC-mediated actin polymerization links Arf and Rac signaling in the cell.
The Human Dendritic Cell Atlas: An integrated transcriptional tool to study human dendritic cell biology

Dendritic cells (DCs) are functionally diverse and are present in most adult tissues, however progress in understanding human DC biology is hampered by a relatively small number of these in circulation and by limited access to human tissues. We built a transcriptional atlas of human DCs by combining samples from 14 expression profiling studies derived from 10 laboratories. We identified significant gene expression variation of DC subset-defining markers across tissue-type and upon viral or bacterial stimulation. We further highlight critical gaps between in vitro-derived DC subsets and their in vivo counterparts and provide evidence that monocytes or cord blood progenitor in vitro-differentiated DCs fail to capture the repertoire of primary DC subsets or behaviours. In constructing a reference DC atlas, we provide an important resource for the community wishing to identify and annotate tissue-specific DC subsets from single-cell datasets, or benchmark new in vitro models of DC biology. Key Points A reference atlas of human DC that allows benchmarking of in vitro DC models Meta-analysis of 14 integrated studies demonstrate that human conventional dendritic cells have distinct tissue-of-origin phenotypes User uploads allow tissue-relevant annotation of human DC subsets from single cell datasets Key subset markers are altered by tissue or activation status Gaps between in vitro-differentiated DC and in vivo counterparts are partially rescued by humanized mouse models, or coculture with NOTCH-ligands.
Nuclear Ribosomal Internal Transcribed Spacer 1 (ITS1) variation in Lady Bird Beetles (Coccinellidae)

The seventeen taxa of the family Coccinellidae were analyzed by sequencing the Internal Transcribed Spacer 1 region followed by analyzing the presence of significantly simple motifs (SSMs), to investigate the presence of functionally important areas in the gene if any and to find phylogenetic inference of the ITSI region between sequenced species. Length comparisons among the ITS 1 region indicated the absence of intraspecific variability. Further, length differences observed were among Adalia bipunctata showing a 3 bp maximum size difference and Psyllobora vigintiduopunctata with 1 bp size difference. The base composition showed highly similar values of A, T, G and C. Except Harmonia axyridis, Phyllobora vigintiduopunctata, Chilocorus renipustulatu, Lemnia duvauceli all other species showed significant number of simple repetitions. Adalia bipunctata showed the highest simple repetition with the RSF value of 1.4440. Thirteen ladybird beetles had higher SSM regions. Adalia bipunctata, Adalia decempunctata, Exochomus quadripustulatus shows high accumulation of AT repeats in 5 prime end flanking region and GC repeats in 3 prime end flanking region. Amida nigropectoralis, Amida quingquefasiata, Menochilus sexmaculata, Phaenochilus mesternalis, Coccidula rufa, Platynaspis luterubra shows a higher concentration of GC repeats towards the 3 prime end flanking regions. Phylogenetic analysis revealed that the tribe Psylloborini of the subfamily Coccinellidae was monophyletic. The members of the Subfamily Chilocorinae first associate with the tribes of subfamily Coccinellidae and then relate with the tribe Scymnini. Exochomus quadripustulatus which shows the highest length variably showed a relationship with Phaenochilus mesternalis 77 bootstrap and 84 posterior probabilities.