Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA sequence-dependent positioning of the linker histone in a nucleosome: a single-pair FRET study

Linker histones (LH) bind to nucleosomes with their globular domain (gH) positioned in either an on- or an off-dyad binding mode. Here, we study the effect of the linker DNA (L-DNA) sequence on the binding of a full-length LH, Xenopus laevis H1.0b, to a Widom 601 nucleosome core particle (ncp) flanked by two 40bp long L-DNA arms, by single-pair FRET spectroscopy. We varied the sequence of the 11bp of L-DNA adjoining the ncp on either side, making the sequence either A-tract, purely GC, or mixed, with 64% AT. The labelled gH consistently exhibited higher FRET efficiency with the labelled L-DNA containing the A-tract, than that with the pure-GC stretch, even when the stretches were swapped. However, it did not exhibit higher FRET efficiency with the L-DNA containing 64% AT-rich mixed DNA when compared to the pure-GC stretch. We explain our observations with a model that shows that the gH binds on-dyad and that two arginines mediate recognition of the A-tract via its characteristically narrow minor groove. To investigate whether this on-dyad minor groove-based recognition was distinct from previously identified off-dyad major groove-based recognition, a nucleosome was designed with A-tracts on both the L-DNA arms. One A-tract was complementary to thymine and the other to deoxyuridine. The major groove of the thymine-tract was lined with methyl groups that were absent from the major groove of the deoxyuridine tract. The gH exhibited similar FRET for both these A-tracts, suggesting that it does not interact with the thymine methyl groups exposed on the major groove. Our observations thus complement previous studies that suggest that different LH isoforms may employ different ways of recognizing AT-rich DNA and A-tracts. This adaptability may enable the LH to universally compact scaffold-associated regions and heterochromatin that are rich in such sequences. Statement of Significance Linker histones (LHs) associate with the smallest repeat unit of chromatin, the nucleosome. They have been observed to have affinity for AT-rich DNA, which is found in heterochromatin and scaffold-associated regions (SAR), which could explain how the LHs can compact such parts of the chromatin. How the LH recognizes such sequences is poorly understood. Using single-pair FRET and modelling, we provide experimental evidence of DNA-sequence-induced changes in the orientation of a LH bound to a nucleosome, and thereby reveal a new mechanism by which the LH can recognize A-tract sequences that are abundantly present in the SAR. Our results show that, depending on how the LH associates with the nucleosome, it can employ more than one mechanism to recognize AT-rich DNA.
Does Short-selling Threat Discipline Managers in Mergers and Acquisitions Decisions?

We explore the disciplining effect of short selling threat on merger and acquisition decisions. Firms with more stock lending supply have higher acquirer returns. We also find lending supply is positively related to Tobin's Q and ROA. Alleviating the endogeneity concern, we find that our results are robust when we use passive institutional ownership and Russell 2000 index inclusion as instrumental variables. Besides, our multivariate difference-in-difference analysis of Reg-SHO PILOT program also provides consistent results. We identify two economic mechanisms through which short selling threat disciplines managers: managers' wealth-performance sensitivity and likelihood of hostile takeovers. Additionally, the disciplinary effect only exists for non-financial-constrained firms and non-all-cash M&A deals.
Mechanism of Schottky barrier formation: The role of amphoteric native defects

A correlation between the Fermi level pinning deduced from Schottky barrier heights and from electrical properties of irradiated III–V semiconductors is found. The correlation indicates that similar defects are responsible for the Fermi level stabilization in both cases. It is proposed that amphoteric native defects, i.e., the defects which change their electrical characteristics depending on the Fermi level position, play a dominant role in the processes leading to a Schottky barrier formation. A detailed analysis of metal–GaAs contacts shows that in this case the amphoteric defects responsible for the barrier heights are VGa (acceptor) and a donor complex AsGa+VAs. It is shown that for thick metal coverages two barriers are formed. A surface barrier determined by the charge associated with a native defect and the bulk barrier controlled by the bulk doping. The sum of the two barrier heights satisfies the Schottky condition for the interface, but it is the bulk barrier that determines the macroscopic ele.
Plasmodesmata-Dependent Intercellular Movement of Bacterial Effectors

Pathogenic microorganisms deliver protein effectors into host cells to suppress host immune responses. Recent findings reveal that phytopathogens manipulate the function of plant cell-to-cell communication channels plasmodesmata (PD) to promote diseases. Several bacterial and filamentous pathogen effectors have been shown to regulate PD in their host cells. A few effectors of filamentous pathogens have been reported to move from the infected cells to neighboring plant cells through PD; however, it is unclear whether bacterial effectors can traffic through PD in plants. In this study, we systemically determined the intercellular movement of Pseudomonas syringae pv. tomato (Pst) DC3000 effectors between adjoining plant cells in Nicotiana benthamiana. We observed that at least 16 Pst DC3000 effectors move from transformed cells to the surrounding plant cells. The movement of the effectors is largely dependent on their molecular weights. The expression of PD regulators, Arabidopsis PD-located protein PDLP5 and PDLP7, lead to PD closure and inhibits the PD-dependent movement of a bacterial effector in N. benthamiana. Similarly, a 22-amino acid peptide of bacterial flagellin (flg22) treatment induces PD closure and suppresses the movement of a bacterial effector in N. benthamiana. Together, our findings demonstrated that bacterial effectors are able to move intercellularly through PD in plants.
Distinct cortical correlation structures of fractal and oscillatory neuronal activity

Electrophysiological population signals contain oscillatory and fractal (1/frequency) components. So far research has largely focused on oscillatory activity and only recently interest in fractal population activity has gained momentum. Accordingly, while the cortical correlation structure of oscillatory population activity has been characterized, little is known about the correlation of fractal neuronal activity. To address this, we investigated fractal neuronal population activity in the human brain using resting-state magnetoencephalography (MEG). We combined source-analysis, signal orthogonalization and irregular-resampling auto-spectral analysis (IRASA) to systematically characterize the cortical distribution and correlation of fractal neuronal activity. We found that fractal population activity is robustly correlated across the cortex and that this correlation is spatially well structured. Furthermore, we found that the cortical correlation structure of fractal activity is similar but distinct from the correlation structure of oscillatory neuronal activity. Anterior cortical regions showed the strongest differences between oscillatory and fractal correlation patterns. Our results suggest that correlations of fractal population activity serve as robust markers of cortical network interactions. Furthermore, our results show that fractal and oscillatory signal components provide non-redundant information about large-scale neuronal correlations. This may reflect at least partly distinct neuronal mechanisms underlying and reflected by oscillatory and fractal neuronal population activity.
CEM500K, a large-scale heterogeneous unlabeled cellular electron microscopy image dataset for deep learning

Automated segmentation of cellular electron microscopy (EM) datasets remains a challenge. Supervised deep learning (DL) methods that rely on region-of-interest (ROI) annotations yield models that fail to generalize to unrelated datasets. Newer unsupervised DL algorithms require relevant pre-training images, however, pre-training on currently available EM datasets is computationally expensive and shows little value for unseen biological contexts, as these datasets are large and homogeneous. To address this issue, we present CEM500K, a nimble 25 GB dataset of 0.5 x 106 unique cellular EM images curated from nearly 600 three-dimensional (3D) and 10,000 two-dimensional (2D) images from >100 unrelated imaging projects. We show that models pre-trained on CEM500K learn features that are biologically relevant and resilient to meaningful image augmentations. Critically, we evaluate transfer learning from these pre-trained models on six publicly available and one newly derived benchmark segmentation task and report state-of-the-art results on each. We release the CEM500K dataset, pre-trained models and curation pipeline for model building and further expansion by the EM community. Data and code are available at https://www.ebi. ac.uk/pdbe/emdb/empiar/entry/10592/ and https://git.io/JLLTz.
Study of metal oxide catalysts by temperature programmed desorption. 4. Oxygen adsorption on various metal oxides

Temperature-programmed desorption of oxygen from 16 metal oxides showed that no significant desorption occurred at 10/sup 0/-560/sup 0/C from V/sub 2/O/sub 5/, MoO/sub 3/, Bi/sub 2/O/sub 3/, WO/sub 3/, and Bi/sub 2/O/sub 3/. 2MoO/sub 3/ (Group A); that varying amounts of oxygen, always amounting to a few per cent of surface coverage, desorbed with up to four desorption peaks from the transition metal oxides Cr/sub 2/O/sub 3/, MnO/sub 2/, Fe/sub 2/O/sub 3/, Co/sub 3/O/sub 4/, NiO, and CuO (Group B); and that oxygen desorbed from TiO/sub 2/, ZnO, SnO/sub 2/, Al/sub 2/O/sub 3/, and SiO/sub 2/ only after evacuation at 600/sup 0/C and oxygen treatment near room temperature (Group C). The desorbed oxygen was probably associated with surface defects such as vacancies, edges, and corners. The amount of oxygen desorbed from Group B and C oxides decreased with increasing heat of oxide formation. Adsorption on silica and alumina was probably physisorption. Adsorption of oxygen on Group A oxides was probably followed by migration into the bulk and incorporation into the lattice. On Group C oxides, the O/sub 2/(-1) ion was directly identified by ESR spectroscopy.
The hidden pangenome: comparative genomics reveals pervasive diversity in symbiotic and free-living sulfur-oxidizing bacteria

Sulfur-oxidizing Thioglobaceae, often referred to as SUP05 and Arctic96BD clades, are widespread and common to hydrothermal vents and oxygen minimum zones. They impact global biogeochemical cycles and exhibit a variety of host-associated and free-living lifestyles. The evolutionary driving forces that led to the versatility, adoption of multiple lifestyles and global success of this family are largely unknown. Here, we perform an in-depth comparative genomic analysis using all available and newly generated Thioglobaceae genomes. Gene content variation was common, throughout taxonomic ranks and lifestyles. We uncovered a pool of variable genes within most Thioglobaceae populations in single environmental samples and we referred to this as the ‘hidden pangenome’. The ‘hidden pangenome’ is often overlooked in comparative genomic studies and our results indicate a much higher intra-specific diversity within environmental bacterial populations than previously thought. Our results show that core-community functions are different from species core genomes suggesting that core functions across populations are divided among the intra-specific members within a population. Defense mechanisms against foreign DNA and phages were enriched in symbiotic lineages, indicating an increased exchange of genetic material in symbioses. Our study suggests that genomic plasticity and frequent exchange of genetic material drives the global success of this family by increasing its evolvability in a heterogeneous environment.
DETECTION OF SURFACE FORCES BY A CELL WALL MECHANOSENSOR

Surface receptors of animal cells, such as integrins, promote mechanosensation by forming local clusters as signaling hubs that transduce tensile forces. Walled cells of plants and fungi also feature surface sensors, with long extracellular domains embedded in their cell wall (CW), thought to detect CW injuries and promote repair. How these sensors probe surface forces remains unknown. By studying the conserved CW sensor Wsc1 in fission yeast, we uncovered the formation of micrometer-sized clusters at sites of local force application onto the CW. These clusters form within minutes of CW compression, in dose-dependence with mechanical stress and dissolve upon stress relaxation. Our data support that Wsc1 senses CW mechanical stress and accumulates to local sites of enhanced stress through its CW-associated extracellular WSC domain, independently of canonical polarity, trafficking and downstream CW regulatory pathways. Wsc1 may represent an autonomous module to detect and transduce local surface forces onto the CW.
Causal relations between cortical network oscillations and breathing frequency

Nasal breathing generates a rhythmic signal which entrains cortical network oscillations in widespread brain regions on a cycle-to-cycle time scale. It is unknown, however, how respiration and neuronal network activity interact on a larger time scale: are breathing frequency and typical neuronal oscillation patterns correlated? Is there any directionality or causal relationship? To address these questions, we recorded field potentials from the posterior parietal cortex of mice together with respiration during REM sleep. In this state, the parietal cortex exhibits prominent theta and gamma oscillations while behavioral activity is minimal, reducing confounding signals. We found that the instantaneous breathing rate strongly correlates with the instantaneous frequency and amplitude of both theta and gamma oscillations. Granger causality analysis revealed specific directionalities for different rhythms: changes in theta activity precede and cause changes in breathing rate, suggesting control of breathing frequency by the functional state of the brain. On the other hand, the instantaneous breathing rate Granger-causes changes in gamma oscillations, suggesting that gamma is influenced by a peripheral reafference signal. These findings show that breathing causally relates to different patterns of rhythmic brain activity, revealing new and complex interactions between elementary physiological functions and neuronal information processing. Significance Statement The study of the interactions between respiration and brain activity has been focused on phase-entrainment relations, in which cortical networks oscillate phase-locked to breathing cycles. Here we discovered new and much broader interactions which link respiration rate (frequency) to different patterns of oscillatory brain activity. Specifically, we show that the instantaneous breathing rate strongly correlates with the instantaneous frequency and amplitude of theta and gamma oscillations, two major network patterns associated with cognitive functions. Interestingly, causality analyses reveal that changes in breathing rate follow theta, suggesting a central drive, while in contrast, gamma activity follows changes in breathing rate, suggesting the role of a reafferent signal. Our results reveal new mechanisms by which nasal breathing patterns may influence brain functions.
DNA metabarcoding provides insights into the diverse diet of a dominant suspension feeder, the giant plumose anemone Metridium farcimen

Benthic suspension feeders have significant impacts on plankton communities by depleting plankton or modifying composition of the plankton through prey selectivity. Quantifying diets of planktivorous animals can be difficult because plankton are frequently microscopic, may lack diagnostic characters, and are digested at variable rates. With DNA metabarcoding, the identification of gut contents has become faster and more accurate, and the technique allows for higher taxonomic resolution-n while also identifying rare and highly degraded items that would otherwise not be detected. We used DNA metabarcoding to examine the diet of the giant plumose anemone Metridium farcimen, a large, abundant, competitively-dominant anemone on subtidal rock surfaces and floating docks in the northeast Pacific Ocean. Gut contents of 12 individuals were compared to 80- and 330-μm filtered plankton samples collected one hour prior between 0.02 and 1.5 km from the anemones. The objectives of this study were to determine if M. farcimen has a selective diet and compare our findings with traditional gut content analyses. Metridium farcimen captured a wider range of prey than previously suspected and metabarcoding found many more taxa than traditional sampling techniques. Gut contents were less diverse than 80-μm filtered plankton samples, but more diverse than 330-μm filtered plankton samples. The diet of the anemones was 52% arthropods with a surprisingly high relative abundance of an ant (10%) that has mating flights in August when this study was conducted. The gut contents of M. farcimen likely include all prey that it can detect and that cannot escape. There were no overrepresented taxa in the gut contents compared to the plankton but there were underrepresented taxa. This study highlights the usefulness of the metabarcoding method in identifying prey within the gut of planktivorous animals and the significant terrestrial input into marine food webs.
Joint species distributions reveal the combined effects of host plants, abiotic factors and species competition as drivers of species abundances in fruit flies

The relative importance of ecological factors and species interactions for phytophagous insect species distributions has long been a controversial issue. Using field abundances of eight sympatric Tephritid fruit flies on 21 host plants, we inferred flies’ realized niches using joint species distribution modelling and network inference, on the community as a whole and separately on three groups of host plants. These inferences were then confronted to flies’ fundamental niches estimated through laboratory-measured fitnesses on host plants. Species abundances were mainly determined by host plants followed by climatic factors, with a minor role for competition between species sharing host plants. The relative importance of these factors mildly changed when we focused on particular host plant groups. Despite overlapping fundamental niches, specialists and generalists had almost distinct realized niches, with possible competitive exclusion of generalists by specialists on Cucurbitaceae, and different assembly rules: specialists were mainly influenced by their adaptation to host plants while generalist abundances varied regardless of their fundamental host use.
Hydration layers trapped between graphene and a hydrophilic substrate

Graphene is mechanically exfoliated on CaF 2 ? > (111) under ambient conditions. We demonstrate the formation of a several monolayer thick hydration layer on the hydrophilic substrate and its response to annealing at temperatures up to 750 K in an ultra-high vacuum environment. Upon heating, water is released, however, it is impossible to remove the first layer. The initially homogeneous film separates into water-containing and water-free domains by two-dimensional Ostwald ripening. Upon severe heating, thick graphene multilayers undergo rupture, while nanoblisters confining sealed water appear on thinner sheets, capable of the storage and release of material. From modeling the dimensions of the nanoblisters, we estimate the graphene/ CaF 2 ? > (111) interfacial adhesion energy to be 0.33 ± 0.13 ? > J m − 2 ? > , thereby viable for polymer-assisted transfer printing.
DeepReading @ SardiStance 2020: Combining Textual, Social and Emotional Features

In this paper we describe our participation to the SardiStance shared task held at EVALITA 2020. We developed a set of classifiers that combined text features, such as the best performing systems based on large pre-trained language models, together with user profile features, such as psychological traits and social media user interactions. The classification algorithms chosen for our models were various monolingual and multilingual Transformer models for text only classification, and XGBoost for the non-textual features. The combination of the textual and contextual models was performed by a weighted voting ensemble learning system. Our approach obtained the best score for Task B, on Contextual Stance Detection.
A crystallographic review of arsenic sulfides: effects of chemical variations and changes induced by exposure to light

Crystal data for natural and synthetic arsenic sulfides are reported and discussed. Most of them [α- and β-dimorphite, realgar, β-As4S4 phase, pararealgar, Kutoglu’s As4S4(II) phase, alacranite, uzonite, orthorhombic As4S5 phase] have a crystal structure consisting of a packing of cage-like, covalently bonded As4Sn (n = 3, 4 and 5) molecules held together by weak interactions of van der Waals character. Their structures are compared in terms of molecular packing and molecular parameters. The layered structural arrangement of orpiment, As2S3, is described and the effects of the incorporation of Se replacing for S is discussed. The structures of wakabayashilite and getchel lite, which contain mixed (As, Sb) coordination polyhedra, are also described to outline the geometric effects of the Sb → As substitution. The results of recent studies dealing with the effects of the exposure of realgar or other arsenic sulfides to visible light are reported and discussed. Their interest in the study of arsenical pigments and their preservation in artwork is outlined with some examples of application.
Compost Effect on Plant Growth-Promoting Rhizobacteria and Mycorrhizal Fungi Population in Maize Cultivations

The composting process allows the conversion of organic waste into organic matter that can be used in counteracting organic matter soil depletion. Moreover, agricultural use of compost increases plants defense abilities against pathogens, leading to a higher crop yield. Key plant growth-promoting rhizobacteria (PGPR) and arbuscular mycorrhial fungi (AMF) populations were evaluated after incorporating high quality composts in both conventional and organic maize production in order to determine if compost application affects the presence of important PGPR and AMF. Results obtained indicate that while the use of the compost as an amendment may exert a limited influence on AMF population, it can significantly modulate the composition of PGPR in the rhizosphere of maize plants.
HaSpeeDe 2 @ EVALITA2020: Overview of the EVALITA 2020 Hate Speech Detection Task

The Hate Speech Detection (HaSpeeDe 2) task is the second edition of a shared task on the detection of hateful content in Italian Twitter messages. HaSpeeDe 2 is composed of a Main task (hate speech detection) and two Pilot tasks, (stereotype and nominal utterance detection). Systems were challenged along two dimensions: (i) time, with test data coming from a different time period than the training data, and (ii) domain, with test data coming from the news domain (i.e., news headlines). Overall, 14 teams participated in the Main task, the best systems achieved a macro F1-score of 0.8088 and 0.7744 on the indomain in the out-of-domain test sets, respectively; 6 teams submitted their results for Pilot task 1 (stereotype detection), the best systems achieved a macro F1-score of 0.7719 and 0.7203 on in-domain and outof-domain test sets. We did not receive any submission for Pilot task 2.