Miracle-dz/UniFAR-FTUs huggingface dataset:
Maternal Protection in Childhood is Associated with Amygdala Reactivity and Structural Connectivity in Adulthood

Recently, we reported that variability in early-life caregiving experiences maps onto individual differences in threat-related brain function. Specifically, we found that greater familial affective responsiveness is associated with increased amygdala reactivity to interpersonal threat, particularly in adolescents having experienced relatively low recent stress. Here, we conceptually replicate and extend on our previous work to provide further evidence that subtle variability in specific features of early caregiving shapes structural and functional connectivity between the amygdala and medial prefrontal cortex (mPFC) in a cohort of 312 young adult volunteers. Multiple regression analyses revealed that participants who reported higher maternal but not paternal protection exhibited increased amygdala reactivity to explicit signals of interpersonal threat (i.e., angry facial expressions) but not implicit signals of broad environmental threat (i.e., fearful facial expressions). While amygdala functional connectivity with regulatory regions of the mPFC was not significantly associated with maternal protection, participants who reported higher maternal protection exhibited relatively decreased structural integrity of the uncinate fasciculus (UF), a white matter tract connecting these same brain regions. The observed associations were independent of the potential confounding influences of participant sex, socioeconomic status, and self-reported childhood trauma. There were no significant associations between structural or functional brain measures and either maternal or paternal care ratings. These findings suggest that an over controlling parenting style in mothers during childhood is associated with functional and structural alterations of brain regions involved in generating and regulating responses to threat in young adulthood.
On cyclic LRC codes that are also LCD codes

Locally recoverable (LRC) codes provide a solution to single node failure in distributed storage systems, where it is a very common problem. On the other hand, linear complementary dual (LCD) codes are useful in fault injections attacks on storage systems. In this paper, we establish a connection between LRC codes and LCD codes. We derive some conditions on the construction of cyclic LRC codes so that they are also LCD codes. A lower bound on the minimum distance of such codes is determined. Some examples have been given to explain the construction.
From Sentiment Annotations to Sentiment Prediction through Discourse Augmentation

Sentiment analysis, especially for long documents, plausibly requires methods capturing complex linguistics structures. To accommodate this, we propose a novel framework to exploit task-related discourse for the task of sentiment analysis. More specifically, we are combining the large-scale, sentiment-dependent MEGA-DT treebank with a novel neural architecture for sentiment prediction, based on a hybrid TreeLSTM hierarchical attention model. Experiments show that our framework using sentiment-related discourse augmentations for sentiment prediction enhances the overall performance for long documents, even beyond previous approaches using well-established discourse parsers trained on human annotated data. We show that a simple ensemble approach can further enhance performance by selectively using discourse, depending on the document length.
Neural networks for classification of strokes in electrical impedance tomography on a 3D head model

We consider the problem of the detection of brain hemorrhages from three-dimensional (3D) electrical impedance tomography (EIT) measurements. This is a condition requiring urgent treatment for which EIT might provide a portable and quick diagnosis. We employ two neural network architectures - a fully connected and a convolutional one - for the classification of hemorrhagic and ischemic strokes. The networks are trained on a dataset with $ 40\, 000 $ samples of synthetic electrode measurements generated with the complete electrode model on realistic heads with a 3-layer structure. We consider changes in head anatomy and layers, electrode position, measurement noise and conductivity values. We then test the networks on several datasets of unseen EIT data, with more complex stroke modeling (different shapes and volumes), higher levels of noise and different amounts of electrode misplacement. On most test datasets we achieve $ \geq 90\% $ average accuracy with fully connected neural networks, while the convolutional ones display an average accuracy $ \geq 80\% $. Despite the use of simple neural network architectures, the results obtained are very promising and motivate the applications of EIT-based classification methods on real phantoms and ultimately on human patients.
MEGA RST Discourse Treebanks with Structure and Nuclearity from Scalable Distant Sentiment Supervision

The lack of large and diverse discourse treebanks hinders the application of data-driven approaches, such as deep-learning, to RST-style discourse parsing. In this work, we present a novel scalable methodology to automatically generate discourse treebanks using distant supervision from sentiment-annotated datasets, creating and publishing MEGA-DT, a new large-scale discourse-annotated corpus. Our approach generates discourse trees incorporating structure and nuclearity for documents of arbitrary length by relying on an efficient heuristic beam-search strategy, extended with a stochastic component. Experiments on multiple datasets indicate that a discourse parser trained on our MEGA-DT treebank delivers promising inter-domain performance gains when compared to parsers trained on human-annotated discourse corpora.
Weighing the Galactic disk in sub-regions of the solar neighbourhood using Gaia DR2

Aims. We infer the gravitational potential of the Galactic disk by analysing the phase-space densities of 120 stellar samples in 40 spatially separate sub-regions of the solar neighbourhood, using Gaia’s second data release (DR2), in order to quantify spatially dependent systematic effects that bias this type of measurement. Methods. The gravitational potential was inferred under the assumption of a steady state in the framework of a Bayesian hierarchical model. We performed a joint fit of our stellar tracers’ three-dimensional velocity distribution, while fully accounting for the astrometric uncertainties of all stars as well as dust extinction, and we also masked angular areas of known open clusters. The inferred gravitational potential is compared, post-inference, to a model for the baryonic matter and halo dark matter components. Results. We see an unexpected but clear trend for all 40 spatially separate sub-regions: Compared to the potential derived from the baryonic model, the inferred gravitational potential is significantly steeper close to the Galactic mid-plane (≲60 pc), but flattens such that the two agree well at greater distances (∼400 pc). The inferred potential implies a total matter density distribution that is highly concentrated to the Galactic mid-plane and decays quickly with height. We see a dependence on the Galactic radius that is consistent with a disk scale length of a few kiloparsecs. Apart from this, there are discrepancies between stellar samples, implying spatially dependent systematic effects which are, at least in part, explained by substructures in the phase-space distributions. Conclusions. In terms of the inferred matter density distribution, the very low matter density that is inferred at greater heights (≳300 pc) is inconsistent with the observed scale height and matter distribution of the stellar disk, which cannot be explained by a misunderstood density of cold gas or other hidden mass. Our interpretation is that these results must be biased by a time-varying phase-space structure, possibly a breathing mode, that is large enough to affect all stellar samples in the same manner.
Why robots should be technical: Correcting mental models through technical architecture concepts

Research in social robotics is commonly focused on designing robots that imitate human behavior. While this might increase a user’s satisfaction and acceptance of robots at first glance, it does not automatically aid a non-expert user in naturally interacting with robots, and might hurt their ability to correctly anticipate a robot’s capabilities. We argue that a faulty mental model, that the user has of the robot, is one of the main sources of confusion. In this work, we investigate how communicating technical concepts of robotic systems to users affect their mental models, and how this can increase the quality of human-robot interaction. We conducted an online study and investigated possible ways of improving users’ mental models. Our results underline that communicating technical concepts can form an improved mental model. Consequently, we show the importance of consciously designing robots that express their capabilities and limitations.
Spiral instabilities: linear and non-linear effects

We present a study of the spiral responses in a stable disc galaxy model to co-orbiting perturbing masses that are evenly spaced around rings. The amplitudes of the responses, or wakes, are proportional to the masses of the perturbations, and we find that the response to a low-mass ring disperses when it is removed – behaviour that is predicted by linear theory. Higher mass rings cause non-linear changes through scattering at the major resonances, provoking instabilities that were absent before the scattering took place. The separate wake patterns from two rings orbiting at differing frequencies produce a net response that is an apparently shearing spiral. When the rings have low mass, the evolution of the simulation is both qualitatively and quantitatively reproduced by linear superposition of the two separate responses. We argue that apparently shearing transient spirals in simulations result from the superposition of two or more steadily rotating patterns, each of which is best accounted for as a normal mode of the non-smooth disc.
On the Analysis of Spatially Constrained Power of Two Choice Policies

We consider a class of power of two choice based assignment policies for allocating users to servers, where both users and servers are located on a two-dimensional Euclidean plane. In this framework, we investigate the inherent tradeoff between the communication cost, and load balancing performance of different allocation policies. To this end, we first design and evaluate a Spatial Power of two (sPOT) policy in which each user is allocated to the least loaded server among its two geographically nearest servers sequentially. When servers are placed on a two-dimensional square grid, sPOT maps to the classical Power of two (POT) policy on the Delaunay graph associated with the Voronoi tessellation of the set of servers. We show that the associated Delaunay graph is 4-regular and provide expressions for asymptotic maximum load using results from the literature. For uniform placement of servers, we map sPOT to a classical balls and bins allocation policy with bins corresponding to the Voronoi regions associated with the second order Voronoi diagram of the set of servers. We provide expressions for the lower bound on the asymptotic expected maximum load on the servers and prove that sPOT does not achieve POT load balancing benefits. However, experimental results suggest the efficacy of sPOT with respect to expected communication cost. Finally, we propose two non-uniform server sampling based POT policies that achieve the best of both the performance metrics. Experimental results validate the effectiveness of our proposed policies.
Innate Immune Effectors Play Essential Roles in Acute Respiratory Infection Caused by Klebsiella pneumoniae

Innate immune effectors constitute the first line of host defense against pathogens. However, the roles of these effectors are not clearly defined during Klebsiella pneumoniae (K. pneumoniae) respiratory infection. In the current study, we established an acute pneumonia model of K. pneumoniae respiratory infection in mice and confirmed that the injury was most severe 48 h post infection. Flow cytometric assay demonstrated that alveolar macrophages were the predominant cells in BALF before infection, and neutrophils were quickly recruited after infection, and this was in consistent with the kinetics of chemokine expression. Further, we depleted neutrophils, macrophages, and complement pathways in vivo and challenged these mice with a sublethal dose of K. pneumonia, the result showed that 80%, 60%, and 40% of mice were died in these groups, respectively, while no deaths occurred in the control group. Besides, innate immune effector depleted mice showed higher bacterial burdens in lungs and blood, companied with more severe lung damage and increased levels of cytokine/chemokine expression. These results demonstrated that the innate immune effectors are critical in the early controlling of K. pneumoniae infection, and neutrophils are the most important. Thus, alternative strategies targeting these innate immune effectors may be effective in controlling of K. pneumoniae respiratory infection.
Phylogenetic measures of indel rate variation among the HIV-1 group M subtypes

The transmission and pathogenesis of human immunodeficiency virus type 1 (HIV-1) is disproportionately influenced by evolution in the five variable regions of the virus surface envelope glycoprotein (gp120). Insertions and deletions (indels) are a significant source of evolutionary change in these regions. However, the influx of indels relative to nucleotide substitutions has not yet been quantified through a comparative analysis of HIV-1 sequence data. Here we develop and report results from a phylogenetic method to estimate indel rates for the gp120 variable regions across five major subtypes and two circulating recombinant forms (CRFs) of HIV-1 group M. We processed over 26,000 published HIV-1 gp120 sequences, from which we extracted 6,605 sequences for phylogenetic analysis. In brief, our method employs maximum likelihood to reconstruct phy-logenies scaled in time and fits a Poisson model to the observed distribution of indels between closely related pairs of sequences in the tree (cherries). The rate estimates ranged from 3.0 × 10−5 to 1.5 × 10−3 indels/nt/year and varied significantly among variable regions and subtypes. Indel rates were significantly lower in the region encoding variable loop V3, and also lower for HIV-1 subtype B relative to other subtypes. We also found that variable loops V1, V2 and V4 tended to accumulate significantly longer indels. Further, we observed that the nucleotide composition of indel sequences was significantly distinct from that of the flanking sequence in HIV-1 gp120. Indels affected potential N-linked glycosylation sites substantially more often in V1 and V2 than expected by chance, which is consistent with positive selection on glycosylation patterns within these regions of gp120. These results represent the first comprehensive measures of indel rates in HIV-1 gp120 across multiple subtypes and CRFs, and identifies novel and unexpected patterns for further research in the molecular evolution of HIV-1.
A hundred new eclipsing binary system candidates studied in a near-infrared window in the VVV survey

Abstract We present the first results obtained from an extensive study of eclipsing binary (EB) system candidates recently detected in the VISTA Variables in the Vía Láctea (VVV) near-infrared (NIR) Survey. We analyse the VVV tile d040 in the southern part of the Galactic disc wherein the interstellar reddening is comparatively low, which makes it possible to detect hundreds of new EB candidates. We present here the light curves and the determination of the geometric and physical parameters of the best candidates found in this ‘NIR window’, including 37 contact, 50 detached, and 13 semi-detached EB systems. We infer that the studied systems have an average of the $K_s$ amplitudes of $0.8$ mag and a median period of 1.22 days where, in general, contact binaries have shorter periods. Using the ‘Physics Of Eclipsing Binaries’ (PHOEBE) interactive interface, which is based on the Wilson and Devinney code, we find that the studied systems have low eccentricities. The studied EBs present mean values of about 5 700 and 4 900 K for the $T_1$ and $T_2$ components, respectively. The mean mass ratio (q) for the contact EB stars is $\sim$ 0.44. This new galactic disk sample is a first look at the massive study of NIR EB systems.
MK-SQuIT: Synthesizing Questions using Iterative Template-filling

The aim of this work is to create a framework for synthetically generating question/query pairs with as little human input as possible. These datasets can be used to train machine translation systems to convert natural language questions into queries, a useful tool that could allow for more natural access to database information. Existing methods of dataset generation require human input that scales linearly with the size of the dataset, resulting in small datasets. Aside from a short initial configuration task, no human input is required during the query generation process of our system. We leverage WikiData, a knowledge base of RDF triples, as a source for generating the main content of questions and queries. Using multiple layers of question templating we are able to sidestep some of the most challenging parts of query generation that have been handled by humans in previous methods; humans never have to modify, aggregate, inspect, annotate, or generate any questions or queries at any step in the process. Our system is easily configurable to multiple domains and can be modified to generate queries in natural languages other than English. We also present an example dataset of 110,000 question/query pairs across four WikiData domains. We then present a baseline model that we train using the dataset which shows promise in a commercial QA setting.
The Physical Role of Mesenchymal Cells Driven by the Actin Cytoskeleton Is Essential for the Orientation of Collagen Fibrils in Zebrafish Fins

Fibrous collagen imparts physical strength and flexibility to tissues by forming huge complexes. The density and orientation of collagen fibers must be correctly specified for the optimal physical property of the collagen complex. However, little is known about its underlying cellular mechanisms. Actinotrichia are collagen fibers aligned at the fin-tip of bony fish and are easily visible under the microscope due to their thick, linear structure. We used the actinotrichia as a model system to investigate how cells manipulate collagen fibers. The 3D image obtained by focused ion beam scanning electron microscopy (FIB-SEM) showed that the pseudopodia of mesenchymal cells encircle the multiple actinotrichia. We then co-incubated the mesenchymal cells and actinotrichia in vitro, and time-lapse analysis revealed how cells use pseudopods to align collagen fiber orientation. This in vitro behavior is dependent on actin polymerization in mesenchymal cells. Inhibition of actin polymerization in mesenchymal cells results in mis-orientation of actinotrichia in the fin. These results reveal how mesenchymal cells are involved in fin formation and have important implications for the physical interaction between cells and collagen fibers.
Actual solubility (S|real.|), level of hydrophilic-lipophilic balance (HLBRequ., HLBD, HLBG) and partition coefficient (log P) of phytochemicals contained in Ext. Camellia sinensis L. aqu. siccum in the light of general Hildebrand-Scatchard-Fedors theory of solubility

Summary Introduction: Using the general Hildebrand-Scatchard-Fedors theory of solubility, the mole fraction (x2) of solubility of phytochemicals contained in the dry green tea leaves was calculated which determines the profile of pharmacological activity. Objective: The applicative purpose of the study was to estimate the actual solubility of phytochemicals – S|real. | [mol/dm3] in water and in water-ethanol solutions of diversified polarity (εM) for their selective extraction and optimal formulation of oral solid dosage form. Methods: The basic physico-chemical and structural quantities of phytochemicals and corresponding mathematical equations of general Hildebrand-Scatchard-Fedors theory of solubility were used to calculate the actual solubility – S|real. | and the level of hydrophilic-lipophilic balance (HLB). Results: The calculated actual solubility values – S|real. | [mol/dm3] collated with correlation equations enabled the assessment of phytochemical capability for the process of mass exchange on phase boundary. Correlation equations for the dependence log P = f (– log S|real.|) point to the structural preferences of phytochemicals in the kinetics of the mass exchange (diffusion) through the natural phase boundary. Conclusions: Calculations and correlations between the values characterizing the actual solubility – S|real. |, media polarity (water, ethanol and their solutions) and the partition coefficient (log P) including the level of hydrophilic-lipophilic balance (HLB) show that basing on thermodynamic components of the general Hildebrand-Scatchard-Fedors theory of solubility, the diffusion profile of phytochemicals contained in the green tea extract (Ext. Camellia sinensis L. aqu. siccum) through the biological phase boundary as well as optimal choice of the extraction medium for selective extraction of the class of phytochemicals can be estimated.
Multidrug-Resistant Hypervirulent Klebsiella pneumoniae Found Persisting Silently in Infant Gut Microbiota

Since the spread of multidrug-resistant Klebsiella pneumoniae (MDRKP) strains is considered as a challenge for patients with weakened or suppressed immunity, the emergence of isolates carrying determinants of hypervirulent phenotypes in addition may become a serious problem even for healthy individuals. The aim of this study is an investigation of the nonoutbreak K. pneumoniae emergence occurred in early 2017 at a maternity hospital of Kazan, Russia. Ten bacterial isolates demonstrating multiple drug resistance phenotypes were collected from eight healthy full-term breastfed neonates, observed at the maternity hospital of Kazan, Russia. All the infants and their mothers were dismissed without symptoms or complaints, in a satisfactory condition. Whole-genome shotgun (WGS) sequencing was performed with the purpose to track down a possible spread source(s) and obtain detailed information about resistance determinants and pathogenic potential of the collected isolates. Microdilution tests have confirmed production of extended-spectrum β-lactamases (ESBL) and their resistance to aminoglycoside, β-lactam, fluoroquinolone, sulfonamide, nitrofurantoin, trimethoprim, and fosfomycin antibiotics and Klebsiella phage. The WGS analysis has revealed the genes that are resistant to aminoglycosides, fluoroquinolones, macrolides, sulfonamides, chloramphenicols, tetracyclines, and trimethoprim and ESBL determinants. The pangenome analysis had split the isolates into two phylogenetic clades. The first group, a more heterogeneous clade, was represented by 5 isolates with 4 different in silico multilocus sequence types (MLSTs). The second group contained 5 isolates from infants born vaginally with the single MLST ST23, positive for genes corresponding to hypervirulent phenotypes: yersiniabactin, aerobactin, salmochelin, colibactin, hypermucoid determinants, and specific alleles of K- and O-antigens. The source of the MDRKP spread was not defined. Infected infants have shown no developed disease symptoms.