Miracle-dz/UniFAR-FTUs huggingface dataset:
A Proinflammatory Immune Response Might Determine Toxoplasma gondii Vertical Transmission and Severity of Clinical Features in Congenitally Infected Newborns

Toxoplasma gondii is the etiological agent of toxoplasmosis. Mother-to-child transmission of this parasite can occur during pregnancy. Newborns with congenital toxoplasmosis may develop central nervous system impairment, with severity ranging from subclinical manifestations to death. A proinflammatory/regulated specific immune profile is crucial in the defense against the parasite; nevertheless, its role in the infected pregnant women and the congenitally infected offspring has been poorly explored, and there is still no consensus about its relation to parasite vertical transmission or to severity and dissemination in the congenitally infected newborns. This work aimed to characterize these relations by means of principal component and principal factor analyses. For this purpose, we determined the specific production of the four immunoglobulin G antibody subclasses, cytokines, and lymphocyte proliferation in the T. gondii–infected pregnant women−10 who transmitted the infection to their offspring and seven who did not—as well as in 11 newborns congenitally infected and grouped according to disease severity (five mild and six moderate/severe) and dissemination (four local and seven disseminated). We found that the immune response of nontransmitter women differed from that of the transmitters, the latter having a stronger proinflammatory response, supporting a previous report. We also found that newborns who developed moderate/severe disease presented higher levels of lymphocyte proliferation, particularly of CD8+ and CD19+ cells, a high proportion of tumor necrosis factor α producers, and reduced expression of the immune modulator transforming growth factor β, as opposed to children who developed mild clinical complications. Our results suggest that a distinctive, not regulated, proinflammatory immune response might favor T. gondii vertical transmission and the development of severe clinical manifestations in congenitally infected newborns.
Phenotypic variation within and across transcriptomic cell types in mouse motor cortex

Cortical neurons exhibit astounding diversity in gene expression as well as in morphological and electrophysiological properties. Most existing neural taxonomies are based on either transcriptomic or morpho-electric criteria, as it has been technically challenging to study both aspects of neuronal diversity in the same set of cells. Here we used Patch-seq to combine patch-clamp recording, biocytin staining, and single-cell RNA sequencing of over 1300 neurons in adult mouse motor cortex, providing a comprehensive morpho-electric annotation of almost all transcriptomically defined neural cell types. We found that, although broad families of transcriptomic types (Vip, Pvalb, Sst, etc.) had distinct and essentially non-overlapping morpho-electric phenotypes, individual transcriptomic types within the same family were not well-separated in the morpho-electric space. Instead, there was a continuum of variability in morphology and electrophysiology, with neighbouring transcriptomic cell types showing similar morpho-electric features, often without clear boundaries between them. Our results suggest that neural types in the neocortex do not always form discrete entities. Instead, neurons follow a hierarchy consisting of distinct non-overlapping branches at the level of families, but can form continuous and correlated transcriptomic and morpho-electrical landscapes within families.
Understanding Crowd Flow Movements Using Active-Langevin Model

Crowd flow describes the elementary group behavior of crowds. Understanding the dynamics behind these movements can help to identify various abnormalities in crowds. However, developing a crowd model describing these flows is a challenging task. In this paper, a physics-based model is proposed to describe the movements in dense crowds. The crowd model is based on active Langevin equation where the motion points are assumed to be similar to active colloidal particles in fluids. The model is further augmented with computer-vision techniques to segment both linear and non-linear motion flows in a dense crowd. The evaluation of the active Langevin equation-based crowd segmentation has been done on publicly available crowd videos and on our own videos. The proposed method is able to segment the flow with lesser optical flow error and better accuracy in comparison to existing state-of-the-art methods.
Clustering of Neural Activity: A Design Principle for Population Codes

We propose that correlations among neurons are generically strong enough to organize neural activity patterns into a discrete set of clusters, which can each be viewed as a population codeword. Our reasoning starts with the analysis of retinal ganglion cell data using maximum entropy models, showing that the population is robustly in a frustrated, marginally sub-critical, or glassy, state. This leads to an argument that neural populations in many other brain areas might share this structure. Next, we use latent variable models to show that this glassy state possesses well-defined clusters of neural activity. Clusters have three appealing properties: (i) clusters exhibit error correction, i.e., they are reproducibly elicited by the same stimulus despite variability at the level of constituent neurons; (ii) clusters encode qualitatively different visual features than their constituent neurons; and (iii) clusters can be learned by downstream neural circuits in an unsupervised fashion. We hypothesize that these properties give rise to a “learnable” neural code which the cortical hierarchy uses to extract increasingly complex features without supervision or reinforcement.
Asteroids’ Size Distribution and Colors from HITS

We report the observations of solar system objects during the 2015 campaign of the High cadence Transient Survey (HiTS). We found 5740 bodies (mostly Main Belt asteroids), 1203 of which were detected in different nights and in g′ and r′. Objects were linked in the barycenter system and their orbital parameters were computed assuming Keplerian motion. We identified 6 near Earth objects, 1738 Main Belt asteroids and 4 Trans-Neptunian objects. We did not find a g′−r′ color–size correlation for 14 < Hg′ < 18 (1 < D < 10 km) asteroids. We show asteroids’ colors are disturbed by HiTS’ 1.6 hr cadence and estimate that observations should be separated by at most 14 minutes to avoid confusion in future wide-field surveys like LSST. The size distribution for the Main Belt objects can be characterized as a simple power law with slope ∼0.9, steeper than in any other survey, while data from the 2014 HiTS campaign has a distribution consistent with previous ones (slopes ∼0.68 at the bright end and ∼0.34 at the faint end). This difference is likely due to the ecliptic distribution of the Main Belt since the 2015 campaign surveyed farther from the ecliptic than did 2014's and most previous surveys.
Pulmonary Pathogens Adapt to Immune Signaling Metabolites in the Airway

A limited number of pulmonary pathogens are able to evade normal mucosal defenses to establish acute infection and then adapt to cause chronic pneumonias. Pathogens, such as Pseudomonas aeruginosa or Staphylococcus aureus, are typically associated with infection in patients with underlying pulmonary disease or damage, such as cystic fibrosis (CF) or chronic obstructive pulmonary disease (COPD). To establish infection, bacteria express a well-defined set of so-called virulence factors that facilitate colonization and activate an immune response, gene products that have been identified in murine models. Less well-understood are the adaptive changes that occur over time in vivo, enabling the organisms to evade innate and adaptive immune clearance mechanisms. These colonizers proliferate, generating a population sufficient to provide selection for mutants, such as small colony variants and mucoid variants, that are optimized for long term infection. Such host-adapted strains have evolved in response to selective pressure such as antibiotics and the recruitment of phagocytes at sites of infection and their release of signaling metabolites (e.g., succinate). These metabolites can potentially function as substrates for bacterial growth and but also generate oxidant stress. Whole genome sequencing and quantified expression of selected genes have helped to explain how P. aeruginosa and S. aureus adapt to the presence of these metabolites over the course of in vivo infection. The serial isolation of clonally related strains from patients with cystic fibrosis has provided the opportunity to identify bacterial metabolic pathways that are altered under this immune pressure, such as the anti-oxidant glyoxylate and pentose phosphate pathways, routes contributing to the generation of biofilms. These metabolic pathways and biofilm itself enable the organisms to dissipate oxidant stress, while providing protection from phagocytosis. Stimulation of host immune signaling metabolites by these pathogens drives bacterial adaptation and promotes their persistence in the airways. The inherent metabolic flexibility of P. aeruginosa and S. aureus is a major factor in their success as pulmonary pathogens.
The local structure of the energy landscape in multiphase mean curvature flow: Weak-strong uniqueness and stability of evolutions

We prove that in the absence of topological changes, the notion of BV solutions to planar multiphase mean curvature flow does not allow for a mechanism for (unphysical) non-uniqueness. Our approach is based on the local structure of the energy landscape near a classical evolution by mean curvature. Mean curvature flow being the gradient flow of the surface energy functional, we develop a gradient-flow analogue of the notion of calibrations. Just like the existence of a calibration guarantees that one has reached a global minimum in the energy landscape, the existence of a "gradient flow calibration" ensures that the route of steepest descent in the energy landscape is unique and stable.
Cognitive Reserve Is Not Associated With Hippocampal Microstructure in Older Adults Without Dementia

Objective Mean Diffusivity (MD) as measured by diffusion tensor imaging (DTI) can be used to detect microstructural alterations of the brain’s gray matter (GM). A previous study found that higher education, which is a proxy for cognitive reserve (CR), was related to decreased hippocampal MD in middle-aged healthy adults, indicating decreased microstructural damage in more educated participants. Based on this study, we aimed at determining the role of hippocampal GM MD in the interaction of AD pathology and CR in older people without dementia. Method We used a sample of 52 cognitively normal people and 38 participants with late mild cognitive impairment (LMCI) from the ADNI database. MCI and cognitively normal participants were analyzed separately. Using linear models, we regressed hippocampal GM MD on CR (quantified by a composite score), amyloid status and the interaction of both, adjusting for age, gender and memory score. Results CR was not associated with hippocampal GM MD and hippocampal GM volume. Also, no interaction of amyloid status and CR was found. Conclusion Our results do not confirm an association of CR and hippocampal GM MD in older adults. In contrast to previous studies, we did not find an association between CR and microstructural, nor macrostructural alterations of the hippocampus in older adults. More research is needed to determine the influence of CR on hippocampal microstructural integrity in relation to age and AD pathology.
Motor Imagery Development in Children: Changes in Speed and Accuracy With Increasing Age

Although motor imagery has been pointed as a promising strategy for the rehabilitation of children with neurological disorders, information on their development throughout childhood and adolescence is still scarce. For instance, it is still unclear at what age they reach a development comparable to the motor imagery performance observed in adults. Herein we used a mental rotation task to assess motor imagery in 164 typically developing children and adolescents, which were divided into four age groups (6–7, 8–9, 10–11, and 12–13 years) and 30 adults. The effects of biomechanical constraints, accuracy, and reaction time of the mental rotation task were considered. ANOVA showed that all groups had the effect of biomechanical restrictions of the mental rotation task. We found a group effect for accuracy [F(4, 180) = 17,560; p < 0.00; η2 = 3.79] and reaction time [F(4, 180) = 17.5; p < 0.001, η2 = 0.615], with the results of children groups 6–7 and 8–9 years being significantly lower than the other groups (p < 0.05). In all the analyses, there were no differences regarding accuracy and reaction time among the participants of the age groups 10–11 and 12–13 years and adults (p > 0.05). Concluding, children aged 6–7 years were able to perform motor imagery, motor imagery ability improved as the participants' ages increased, and children aged 10 and over-performed similarly to adults.
Statistical and Topological Properties of Sliced Probability Divergences

The idea of slicing divergences has been proven to be successful when comparing two probability measures in various machine learning applications including generative modeling, and consists in computing the expected value of a `base divergence' between one-dimensional random projections of the two measures. However, the computational and statistical consequences of such a technique have not yet been well-established. In this paper, we aim at bridging this gap and derive some properties of sliced divergence functions. First, we show that slicing preserves the metric axioms and the weak continuity of the divergence, implying that the sliced divergence will share similar topological properties. We then precise the results in the case where the base divergence belongs to the class of integral probability metrics. On the other hand, we establish that, under mild conditions, the sample complexity of the sliced divergence does not depend on the dimension, even when the base divergence suffers from the curse of dimensionality. We finally apply our general results to the Wasserstein distance and Sinkhorn divergences, and illustrate our theory on both synthetic and real data experiments.
Consequences of preserving reversibility in quantum superchannels

Similarly to quantum states, quantum operations can also be transformed by means of quantum superchannels, also known as process matrices. Quantum superchannels with multiple slots are deterministic transformations which take causally independent quantum operations as inputs and are enforced to respect the laws of quantum mechanics but the use of input operations may lack a definite causal order. While causally ordered superchannels admit a characterization in terms of quantum circuits, a similar characterization of general superchannels in terms of standard quantum objects with a clearer physical interpretation has been missing. In this paper we provide a mathematical characterization for pure superchannels with two slots (also known as bipartite pure processes), which are superchannels preserving the reversibility of quantum operations. We show that the reversibility preserving condition restricts all pure superchannels with two slots to be either a causally ordered quantum circuit only consisting of unitary operations or a coherent superposition of two pure causally ordered circuits. The latter may be seen as a generalization of the quantum switch, allowing a physical interpretation for pure two-slot superchannels. An immediate corollary is that purifiable bipartite processes cannot violate device-independent causal inequalities.
Risk assessment of heavy metal pollution in water, sediment and plants in the Nile River in the Cairo region, Egypt

Abstract Samples of water, sediment and two native plants (Eichhornia crassipes and Ceratophyllum demersum), collected seasonally from eight sites, were analyzed to investigate the level of contamination with metals (Fe, Mn, Ni, Co, Zn, Cu, Cr, Pb and Cd) in the Nile River in the Cairo region, using heavy metal pollution and contamination indices in the case of water, and the geoaccumulation index, the pollution load index, the enrichment factor and the potential ecological risk factor in the case of sediment. The results clarified that the levels of metals among three compartments were in order: sediments > plants > water. The Nile water in Cairo is not critically polluted by the studied metals and the metal pollution index for most sites does not exceed the critical limit (< 100). Sediment samples showed a clear accumulation of Mn, Ni and Cd when compared with benchmarks cited by the Environmental Protection Agency (EPA), especially during low flow seasons. The contribution of Cd to the ecological risk assessment was about 80%, while the contribution of Ni was about 10%, reflecting that these elements originated primarily from anthropogenic sources. Eichhornia crassipes and Ceratophyllum demersum have a higher accumulation capacity for Mn, Cu and Fe compared to the other studied metals.
A surprising mechanism lacking the Ni(0) state during the Ni(II)-catalyzed P–C cross-coupling reaction performed in the absence of a reducing agent – An experimental and a theoretical study

Abstract The Hirao reaction, i.e. the P–C coupling between a bromoarene and a >P(O)H reagent performed in most cases in the presence of a Pd(0) complex incorporating a P-ligand may also be carried out applying a Ni(II) catalyst precursor with or without Zn or Mg as the reducing agent. The Ni catalysts may include P- or N-ligands. B3LYP/6-31G(d,p)//PCM(MeCN) quantum chemical calculations suggested that the mechanism of the NiX2 catalyzed (X=Cl or Br) P–C couplings performed in the absence of a reducing agent, and in the excess of the >P(O)H reagent serving as the P-ligand (via its tautomeric >POH form) is completely different from that of the Pd(OAc)2 promoted version, as no reduction of the Ni(II) occurs. In the two variations mentioned, the active catalyst is the dehydrobrominated species derived from primary complex [(HO)Y2P]2Ni(II)Br2, and the [(HO)Y2P]2Pd(0) complex itself, respectively. Both species undergo temporary oxidation (to “Ni(IV)” and “Pd(II)”, respectively) in the catalytic cycle. During the catalysis with “P2Ni(II)X2”, one of the P-ligands serves the >P(O)H function of the ArP(O)H < product. The consequence of this difference is that in the Ni(II)-catalyzed case, somewhat less >P(O)H-species is needed than in the Pd(0)-promoted instance. Applying 10 % of the Pd(OAc)2 or NiX2 precursor, the optimum quantity of the P-reagent is 1.3 equivalent and, in the first approach, 1.1 equivalent, respectively. Preparative experiments justified the new mechanism explored. The ligation of Ni(II) was also investigated by theoretical calculations. It was proved that the bis-complexation is the most favorable energetically as compared to the mono-, tri- and tetra-ligation.
Examining the Causal Effects of Sleep Deprivation on Emotion Regulation and Its Neural Mechanisms

Abstract Cognitive reappraisal (CR) is a strategy used to regulate emotions that is thought to be effective but effortful, relying on higher-order cognitive control systems to engage in active regulation. Sleep deprivation is believed to impair the functioning of these control systems, suggesting that it may impede the ability to implement CR effectively. This study tested the causal effects of sleep deprivation on emotional reactivity and the neurobiological systems underlying CR. We employed a within-subject crossover design in which participants underwent fMRI scanning twice, once when fully rested and once after a night of total sleep deprivation. During scans, participants passively viewed or used CR to down-regulate their emotional response to negative and neutral images. Contrary to hypotheses, both self-reported negative affect ratings and neural responses to the images indicated no difference in the way participants implemented CR when sleep deprived and when fully rested. Meanwhile, neural regions that showed distinct reactivity responses to negative relative to neutral images lost this specificity under deprived conditions. Negative affect ratings and heart rate deceleration, a physiological response typically evoked by aversive pictures, exhibited a similar blunting. Together, these results suggest that, although sleep deprivation may reduce the discrimination between emotional reactivity responses to negative and neutral stimuli, it does not impact CR the way it is presently studied.
On n-semiprimary ideals and n-pseudo valuation domains

Abstract Let R be a commutative ring with and n a positive integer. A proper ideal I of R is an n-semiprimary ideal of R if whenever for then or Let R be an integral domain with quotient field K. A proper ideal I of R is an n-powerful ideal of R if whenever for then or and I is an n-powerful semiprimary ideal of R if whenever for then or If every prime ideal of R is an n-powerful semiprimary ideal of R, then R is an n-pseudo-valuation domain (n-PVD). In this paper, we study the above concepts and relate them to several generalizations of pseudo-valuation domains.
Verbal Working Memory as Emergent from Language Comprehension and Production

This article reviews current models of verbal working memory and considers the role of language comprehension and long-term memory in the ability to maintain and order verbal information for short periods of time. While all models of verbal working memory posit some interaction with long-term memory, few have considered the character of these long-term representations or how they might affect performance on verbal working memory tasks. Similarly, few models have considered how comprehension processes and production processes might affect performance in verbal working memory tasks. Modern theories of comprehension emphasize that people learn a vast web of correlated information about the language and the world and must activate that information from long-term memory to cope with the demands of language input. To date, there has been little consideration in theories of verbal working memory for how this rich input from comprehension would affect the nature of temporary memory. There has also been relatively little attention to the degree to which language production processes naturally manage serial order of verbal information. The authors argue for an emergent model of verbal working memory supported by a rich, distributed long-term memory for language. On this view, comprehension processes provide encoding in verbal working memory tasks, and production processes maintenance, serial ordering, and recall. Moreover, the computational capacity to maintain and order information varies with language experience. Implications for theories of working memory, comprehension, and production are considered.