Miracle-dz/UniFAR-FTUs huggingface dataset:
AcCompl-it @ EVALITA2020: Overview of the Acceptability & Complexity Evaluation Task for Italian

The Acceptability and Complexity evaluation task for Italian (AcCompl-it) was aimed at developing and evaluating methods to classify Italian sentences according to Acceptability and Complexity. It consists of two independent tasks asking participants to predict either the acceptability or the complexity rate (or both) of a given set of sentences previously scored by native speakers on a 1-to-7 points Likert scale. In this paper, we introduce the datasets distributed to the participants, we describe the different approaches of the participating systems and provide a first analysis of the obtained results.
The landscape of driver mutations in cutaneous squamous cell carcinoma

Cutaneous squamous cell carcinoma is a form of skin cancer originating from keratinocytes in the skin. It is the second most common type of cancer and is responsible for an estimated 8000 deaths per year in the United States. Compared to other cancer subtypes with similar incidences and death tolls, our understanding of the somatic mutations driving cutaneous squamous cell carcinoma is limited. The main challenge is that these tumors have high mutation burdens, primarily a consequence of UV-radiation-induced DNA damage from sunlight, making it difficult to distinguish driver mutations from passenger mutations. We overcame this challenge by performing a meta-analysis of publicly available sequencing data covering 105 tumors from 10 different studies. Moreover, we eliminated tumors with issues, such as low neoplastic cell content, and from the tumors that passed quality control, we utilized multiple strategies to reveal genes under selection. In total, we nominated 30 cancer genes. Among the more novel genes, mutations frequently affected EP300 , PBRM1 , USP28 , and CHUK . Collectively, mutations in the NOTCH and p53 pathways were ubiquitous, and to a lesser extent, mutations affected genes in the Hippo pathway, genes in the Ras/MAPK/PI3K pathway, genes critical for cell-cycle checkpoint control, and genes encoding chromatin remodeling factors. Taken together, our study provides a catalog of driver genes in cutaneous squamous cell carcinoma, offering points of therapeutic intervention and insights into the biology of cutaneous squamous cell carcinoma.
Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases

T cells are involved in control of SARS-CoV-2 infection. To establish the patterns of immunodominance of different SARS-CoV-2 antigens, and precisely measure virus-specific CD4+ and CD8+ T cells, we studied epitope-specific T cell responses of approximately 100 convalescent COVID-19 cases. The SARS-CoV-2 proteome was probed using 1,925 peptides spanning the entire genome, ensuring an unbiased coverage of HLA alleles for class II responses. For HLA class I, we studied an additional 5,600 predicted binding epitopes for 28 prominent HLA class I alleles, accounting for wide global coverage. We identified several hundred HLA-restricted SARS-CoV-2-derived epitopes. Distinct patterns of immunodominance were observed, which differed for CD4+ T cells, CD8+ T cells, and antibodies. The class I and class II epitopes were combined into new epitope megapools to facilitate identification and quantification of SARS-CoV-2-specific CD4+ and CD8+ T cells.
Italian Transformers Under the Linguistic Lens

In this paper we present an in-depth investigation of the linguistic knowledge encoded by the transformer models currently available for the Italian language. In particular, we investigate whether and how using different architectures of probing models affects the performance of Italian transformers in encoding a wide spectrum of linguistic features. Moreover, we explore how this implicit knowledge varies according to different textual genres.
"Il Mago della Ghigliottina" @ GhigliottinAI: When Linguistics meets Artificial Intelligence

English. This paper describes Il mago della Ghigliottina , a bot which took part in the Ghigliottin-AI task of the Evalita 2020 evaluation campaign. The aim is to build a system able to solve the TV game “La Ghigliottina”. Our system has already participated in the Evalita 2018 task NLP4FUN . Compared to that occasion, it improved its accuracy from 61% to 68.6%. Italiano. Questo contributo descrive Il mago della Ghigliottina, un bot che ha partecipato a Ghigliottin-AI, uno dei task di Evalita 2020. Scopo del task è mettere in piedi un sistema automatico capace di risolvere il gioco televisivo “La Ghigliot-tina”. Il nostro sistema ha già parteci-pato all’edizione del 2018 di Evalita al task NLP4FUN. Rispetto all’edizione del 2018 di NLP4FUN, l’accuratezza è salita dal 61% al 68.6%.
Soft sweeps predominate recent positive selection in bonobos (Pan paniscus) and chimpanzees (Pan troglodytes)

Two modes of positive selection have been recognized: 1) hard sweeps that result in the rapid fixation of a beneficial allele typically from a de novo mutation and 2) soft sweeps that are characterized by intermediate frequencies of at least two haplotypes that stem from standing genetic variation or recurrent de novo mutations. While many populations exhibit both hard and soft sweeps throughout the genome, there is increasing evidence that soft sweeps, rather than hard sweeps, are the predominant mode of adaptation in many species, including humans. Here, we use a supervised machine learning approach to assess the extent of completed hard and soft sweeps in the closest living relatives of humans: bonobos and chimpanzees (genus Pan). We trained convolutional neural network classifiers using simulated data and applied these classifiers to population genomic data for 71 individuals representing all five extant Pan lineages, of which we successfully analyzed 60 individuals from four lineages. We found that recent adaptation in Pan is largely the result of soft sweeps, ranging from 73.1 to 97.7% of all identified sweeps. While few hard sweeps were shared among lineages, we found that between 19 and 267 soft sweep windows were shared by at least two lineages. We also identify novel candidate genes subject to recent positive selection. This study emphasizes the importance of shifts in the physical and social environment, rather than novel mutation, in shaping recent adaptations in bonobos and chimpanzees.
AIM: A network model of attention in auditory cortex

Attentional modulation of cortical networks is critical for the cognitive flexibility required to process complex scenes. Current theoretical frameworks for attention are based almost exclusively on studies in visual cortex, where attentional effects are typically modest and excitatory. In contrast, attentional effects in auditory cortex can be large and suppressive. A theoretical framework for explaining attentional effects in auditory cortex is lacking, preventing a broader understanding of cortical mechanisms underlying attention. Here, we present a cortical network model of attention in primary auditory cortex (A1). A key mechanism in our network is attentional inhibitory modulation (AIM) of cortical inhibitory neurons. In this mechanism, top-down inhibitory neurons disinhibit bottom-up cortical circuits, a prominent circuit motif observed in sensory cortex. Our results reveal that the same underlying mechanisms in the AIM network can explain diverse attentional effects on both spatial and frequency tuning in A1. We find that a dominant effect of disinhibition on cortical tuning is suppressive, consistent with experimental observations. Functionally, the AIM network may play a key role in solving the cocktail party problem. We demonstrate how attention can guide the AIM network to monitor an acoustic scene, select a specific target, or switch to a different target, providing flexible outputs for solving the cocktail party problem.
Industry Best Practices for Component Approval in FLOSS Governance

Increasingly companies realize the value of using free/libre and open source software (FLOSS) in their products, but need to manage the associated risks. Leading companies introduce open source governance as a solution. A key aspect of corporate FLOSS governance deals with choosing and evaluating open source components for use in products. Following an industry-based research approach, we present 13 best practices in the pattern format of context-problem-solutions paired with consequences. In this paper, we cover an excerpt of the Component Approval section of our FLOSS governance handbook. This article builds upon our previous EuroPLoP publication covering Component Reuse in FLOSS governance processes, as well as other publications on the topic. Analyzing qualitative data gathered from 15 expert interviews, we derive and interconnect the common industry recommendations for reviewing, tracking, and approving open source components in a company environment. We conclude by presenting workflow templates that put various best practices in relation to each other.
ArchiMeDe @ DANKMEMES: A New Model Architecture for Meme Detection

English. We introduce ArchiMeDe, a multimodal neural network-based architecture used to solve the DANKMEMES meme detections subtask at the 2020 EVALITA campaign. The system incor-porates information from visual and textual sources through a multimodal neural ensemble to predict if input images and their respective metadata are memes or not. Each pre-trained neural network in the ensemble is ﬁrst ﬁne-tuned indi-vidually on the training dataset to perform domain adaptation. Learned text and visual representations are then concatenated to obtain a single multimodal embedding
Equilibrium and Kinetic Study on Reactive Dyes Adsorption by Palm Kernel Shell-Based Activated Carbon: In Single and Binary Systems

The adsorption of two reactive dyes, Reactive Black 5 and Reactive Red E, onto palm kernel shell-activated carbon (PKSAC) was studied. The effect of the presence of more than one dye in solution on the equilibrium and kinetics of adsorption was investigated. Equilibrium isotherm models were applied to describe the adsorption capacities of single and binary systems. Adsorption of reactive dyes for single system can be represented by the Freundlich and the Redlich-Peterson models. For binary system, the equilibrium was described successfully by the modified extended Freundlich model. Experimental data showed that competitive adsorption for active sites on the carbon surface resulted in a reduction in the overall uptake capacity of the reactive dyes. The rates of adsorption in single system were found to agree well with the pseudosecond-order kinetic model. Finally, the chemical oxygen demand (COD) of the treated reactive dye solutions from single and binary systems showed that a minimum of 4 g/L dosage of PKSAC was needed to reduce the COD to an acceptable level according to the Water Quality Guidelines and the Pollutant Fact Sheets Guidelines.
Transcriptional responses to arbuscular mycorrhizal symbiosis development are conserved in the early divergent Marchantia paleacea

Arbuscular mycorrhizal symbiosis (AMS) arose in land plants more than 400 million years ago, perhaps acting as a major contributor to plant terrestrialization. The ability to engage in AMS is evolutionarily conserved across most clades of extant land plants, including early diverging bryophytes. Despite its broad taxonomic distribution, little is known about the molecular components that underpin AMS in early diverging land plants as the mechanisms regulating the symbiosis were primarily characterized in angiosperms. Several AMS associated genes were recently shown to be conserved in liverworts and hornworts, but evidence of them being associated with symbiosis in bryophytes is scarce. In this study, we characterised the dynamic response of the liverwort Marchantia paleacea to Rhizophagus irregularis colonization by time-resolved transcriptomics across progressive stages of symbiosis development. Gene orthology inference and comparative analysis of the M. paleacea transcriptional profile with a well characterised legume model -Medicago truncatula - revealed a deep conservation of transcriptional responses to AMS across distantly related species. We identified evolutionarily conserved patterns of expression of genes required for pre-symbiotic signalling, intracellular colonization and symbiotic nutrient exchange. Our study demonstrates that the genetic machinery regulating key aspects of symbiosis in plant hosts is largely conserved and coregulated across distantly related land plants. If bryophytes are confirmed to be monophyletic, our analysis provides novel insights on the first molecular pathways associated with symbiosis at the dawn of plant colonization of land. Significance Statement Arbuscular mycorrhizal symbiosis (AMS) between plants and soil fungi was proposed as one of the key adaptations enabling land colonization by plants. The symbiosis is widespread across most extant plant clades, including early-diverging bryophytes, suggesting that it evolved before the last common ancestor of land plants. Recent phylogenetic analyses uncovered that genes regulating AMS in angiosperms are present in the genomes of bryophytes. Our work shows that a set of these genes are transcriptionally induced during AMS in liverworts. Based on the conservation of their transcriptional profiles across land plants, we propose that these genes acquired an AMS-associated function before the last common ancestor of land plants.
Data-independent Acquisition-based Proteome and Phosphoproteome Profiling across Six Melanoma Cell Lines Reveals Determinants of Proteotypes

Human cancer cell lines are widely used in pharmacological and systems biological studies. The rapid documentation of the steady-state gene expression landscape of the cells used in a particular experiment may help to improve the reproducibility of scientific research. Here we applied a data-independent acquisition mass spectrometry (DIA-MS) method, coupled with a peptide spectral-library free data analysis workflow, to measure both proteome and phosphoproteome of a melanoma cell line panel with different metastatic properties. For each cell line, the single-shot DIA-MS detected 8,100 proteins and almost 40,000 phosphopeptides in the respective measurement of two hours. Benchmarking the DIA-MS data towards the RNA-seq data and tandem mass tag (TMT)-MS results from the same set of cell lines demonstrated comparable qualitative coverage and quantitative reproducibility. Our data confirmed the high but complex mRNA~protein and protein~phospsite correlations. The results successfully established DIA-MS as a strong and competitive proteotyping approach for cell lines. The data further showed that all subunits of Glycosylphosphatidylinositol (GPI)-anchor transamidase complex were overexpressed in metastatic melanoma cells and identified altered phosphoprotein modules such as BAF complex and mRNA splicing between metastatic and primary cells. This study provides a high-quality resource for calibrating DIA-MS performance, benchmarking DIA bioinformatic algorithms, and exploring the metastatic proteotypes in melanoma cells.
Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain

Transposable elements (TEs) constitute 50% of the human genome and many have been co-opted throughout human evolution due to gain of advantageous regulatory functions controlling gene expression networks. Several lines of evidence suggest these networks can be fine-tuned by the largest family of TE controllers, the KRAB-containing zinc finger proteins (KZFPs). One tissue permissive for TE transcriptional activation (termed ‘transposcription’) is the adult human brain, however comprehensive studies on the extent of this process and its potential contribution to human brain development are lacking. In order to elucidate the spatiotemporal transposcriptome of the developing human brain, we have analysed two independent RNA-seq datasets encompassing 16 distinct brain regions from eight weeks post-conception into adulthood. We reveal an anti-correlated, KZFP:TE transcriptional profile defining the late prenatal to early postnatal transition, and the spatiotemporal and cell type specific activation of TE-derived alternative promoters driving the expression of neurogenesis-associated genes. We also demonstrate experimentally that a co-opted antisense L2 element drives temporal protein re-localisation away from the endoplasmic reticulum, suggestive of novel TE dependent protein function in primate evolution. This work highlights the widespread dynamic nature of the spatiotemporal KZFP:TE transcriptome and its potential importance throughout neurotypical human brain development.
InAs/GaAs Quantum Dots Grown by Metalorganic Chemical Vapor Deposition

InAs quantum dots (QDs) have been grown by metalorganic chemical vapor deposition on exactly (001) oriented GaAs using the Stranski-Krastanow growth mode. The samples exhibit a high average dot density of 4 x 10 10 cm -2 with no defects over macroscopic areas. The QDs show bright room temperature luminescence at around 1.1 eV. Vertical dot stacks consisting of up to 5 QD sheets with various GaAs separation layer thicknesses have been produced. Transmission eletron microscope images show pronounced QD ordering in the growth direction. For thin separation layers the dot luminescence is red shifted by ∼70 meV for the stacked dots as compared to single dot sheets. A low threshold (100 A/cm 2 at 77K) separate confinement heterojunction laser with a five-fold dot stack as an active medium operating at up to room temperature is demonstrated.
Design of a radial multi-offset detection pattern for in vivo phase contrast imaging of the retinal ganglion cells in humans

Previous work has shown that multi-offset detection in adaptive optics scanning laser ophthalmoscopy (AOSLO) can be used to image retinal ganglion cells (RGCs) in monkeys and humans. However, though images of RGCs in anesthetized monkeys with high light levels produced high contrast images of RGCs, images from humans failed to reach the same contrast due to several drawbacks in the previous dual-wavelength multi-offset approach. Our aim here was to design and build a multi-offset detection pattern for humans at safe light levels that could reveal the retinal ganglion cell layer neurons with a contrast, robustness and acquisition time approaching results only previously obtained in monkeys. Here, we present a new imaging system using only one light source, compared to the previous dual-wavelength used on monkeys. Our single-wavelength solution allows for increased light power and eliminates problematic chromatic aberrations. Then, we demonstrate that a radial multi-offset detection pattern with an offset distance of 8-10 Airy Disk Diameter (ADD) is optimal to detect photons multiply scattered in all directions from RGCs thereby enhancing their contrast. This new setup and image processing pipeline led to improved imaging of retinal ganglion cells using multi-offset imaging in AOSLO.
Cold‐drawing of glass‐like and crystalline polymers

Solid polymers—both glass-like and crystalline—can be cold-drawn. In addition to studies of the specific aspects of this process in individual cases, as governed by structural features, the development of a theory of cold-drawing requires an investigation of the general laws of this process. According to the experimental conditions used, cold-drawing may be carried out either isothermally (at low rates of drawing and with good heat dispersion) or non-isothermally. A number of specific features of the non-isothermal process may be explained by a temperature increase in the stressed region; this has in fact been done in published work on this subject. However, the basic features of this phenomenon persist, as has been shown experimentally, in the isothermal cold-drawing of both glass-like and crystalline polymers. These features include: (a) the possibility of cold-drawing, with large residual deformations; (b) the character of the stress—deformation curves; (c) a displacement at the beginning, and a homogeneous or inhomogeneous stretching over the further course of the cold-drawing (both possibilities being realized in either type of polymer—glass-like or crystalline); (d) the effect of temperature and the rate of drawing on the initial stress σB. These phenomena must be interpreted in a way which does not involve the assumption of a temperature rise. The values of σB depends on the rate of drawing v, this dependence being expressed by the relation σB = A + B log v, valid for both glass-like and crystalline polymers. The two types differ only in the value of the constant B, which is lower for crystalline polymers (polyethylene, polyamide, crystalline silicone rubber) than for glass-like polymers (polyvinyl chloride, amorphous silicone rubber, polymethyl methacrylate, butadiene-acrylonitrile copolymer, etc.). Crystalline and glass-like polymers differ in their mechanisms of cold-drawing. Crystalline polymers, as is well known, undergo recrystallization on deformation; in either type, however, there is a rupture of intermolecular bonds by stresses. Hence follows the kinetic, relaxational character of cold-drawing. The dependence of σB on the temperature and rate of drawing may be explained on the assumption that the activation energy of the molecular rearrangement is decreased with increasing stresses. Uniform isothermal stretchig is, generally speaking, unstable. The fact that it may be realized in practice, and also the stabilization of the block in non-uniform drawing, makes it necessary to assume that the mechanical relaxation properties of the polymer change on orientation.