Miracle-dz/UniFAR-FTUs huggingface dataset:
ALMA resolves the hourglass magnetic field in G31.41+0.31

Context. Submillimeter Array (SMA) 870 μm polarization observations of the hot molecular core G31.41+0.31 revealed one of the clearest examples up to date of an hourglass-shaped magnetic field morphology in a high-mass star-forming region. Aims. To better establish the role that the magnetic field plays in the collapse of G31.41+0.31, we carried out Atacama Large Millimeter/ submillimeter Array (ALMA) observations of the polarized dust continuum emission at 1.3 mm with an angular resolution four times higher than that of the previous (sub)millimeter observations to achieve an unprecedented image of the magnetic field morphology. Methods. We used ALMA to perform full polarization observations at 233 GHz (Band 6). The resulting synthesized beam is 0′′. 28×0′′. 20 which, at the distance of the source, corresponds to a spatial resolution of ~875 au. Results. The observations resolve the structure of the magnetic field in G31.41+0.31 and allow us to study the field in detail. The polarized emission in the Main core of G31.41+0.41is successfully fit with a semi-analytical magnetostatic model of a toroid supported by magnetic fields. The best fit model suggests that the magnetic field is well represented by a poloidal field with a possible contribution of a toroidal component of ~10% of the poloidal component, oriented southeast to northwest at approximately −44° and with an inclination of approximately −45°. The magnetic field is oriented perpendicular to the northeast to southwest velocity gradient detected in this core on scales from 103 to 104 au. This supports the hypothesis that the velocity gradient is due to rotation of the core and suggests that such a rotation has little effect on the magnetic field. The strength of the magnetic field estimated in the central region of the core with the Davis–Chandrasekhar-Fermi method is ~8–13 mG and implies that the mass-to-flux ratio in this region is slightly supercritical. Conclusions. The magnetic field in G31.41+0.31 maintains an hourglass-shaped morphology down to scales of <1000 au. Despite the magnetic field being important in G31.41+0.31, it is not enough to prevent fragmentation and collapse of the core, as demonstrated by the presence of at least four sources embedded in the center of the core.
Kind theory

My contribution, described in this thesis, is a theory that is meant to assist in the construction of complex software systems. I propose a notion of structure that is independent of language, formalism, or problem domain. I call this new abstraction a kind, and its related formal system, kind theory. I define a type system that models the structural aspects of kind theory. I also define an algebra that models this type system and provides a logic in which one can specify and execute computations. A reflective definition of kind theory is reviewed. This reflective specification depends upon a basic ontology for mathematics. By specifying the theory in itself, I provide an example of how one can use kind theory to reason about reuse in general formal systems. I provide examples of the use of kind theory in reasoning about software constructs in several domains of software engineering. I also discuss a set of software tools that I have constructed that realize or use kind theory. A logical framework is used to specify a type theoretic and algebraic model for the theory. Using this basic theorem prover one can reason about software systems using kind theory. Also, I have constructed a reuse repository that supports online collaboration, houses software assets, helps search for components that match specifications, and more. This repository is designed to use kind theory (via the logical framework) for the representation of, and reasoning about, software assets. Finally, I propose a set of language-independent specification constructs called semantic properties which have a semantics specified in kind theory. I show several uses of these constructs, all of which center on reasoning about reusable component-based software, by giving examples of how these constructs are applied to programming and specification languages. I discuss how the availability of these constructs and the associated theory impact the software development process.
Social coding of the multisensory space around us

Multisensory integration of stimuli occurring in the area surrounding our bodies gives rise to the functional representation of peripersonal space (PPS). PPS extent is flexible according to the affective context and the target of an action, but little is known about how social context modulates it. We used an audiotactile interaction task to investigate PPS of individuals during social interaction. Participants had to detect as fast as possible a tactile stimulus while task-irrelevant looming sounds were presented, while they were paired as collaborative dyads and as competitive dyads. We also measured PPS in participants seated near an inactive individual. PPS boundaries were modulated only when participants collaborated with a partner, in the form of an extension on the right hemispace and independently of the location of the partner. This suggests that space processing is modified during collaborative tasks. During collective actions, a supra-individual representation of the space of action could be at stake in order to adapt our individual motor control to an interaction as a group with the external world. Reassessing multisensory integration in the light of its potential social sensitivity might reveal that low-level mechanisms are modified by the need to interact with others.
Consistency of co-occurring actions influences young children’s word learning

Communication with young children is often multimodal in nature, involving, for example, language and actions. The simultaneous presentation of information from both domains may boost language learning by highlighting the connection between an object and a word, owing to temporal overlap in the presentation of multimodal input. However, the overlap is not merely temporal but can also covary in the extent to which particular actions co-occur with particular words and objects, e.g. carers typically produce a hopping action when talking about rabbits and a snapping action for crocodiles. The frequency with which actions and words co-occurs in the presence of the referents of these words may also impact young children’s word learning. We, therefore, examined the extent to which consistency in the co-occurrence of particular actions and words impacted children’s learning of novel word–object associations. Children (18 months, 30 months and 36–48 months) and adults were presented with two novel objects and heard their novel labels while different actions were performed on these objects, such that the particular actions and word–object pairings always co-occurred (Consistent group) or varied across trials (Inconsistent group). At test, participants saw both objects and heard one of the labels to examine whether participants recognized the target object upon hearing its label. Growth curve models revealed that 18-month-olds did not learn words for objects in either condition, and 30-month-old and 36- to 48-month-old children learned words for objects only in the Consistent condition, in contrast to adults who learned words for objects independent of the actions presented. Thus, consistency in the multimodal input influenced word learning in early childhood but not in adulthood. In terms of a dynamic systems account of word learning, our study shows how multimodal learning settings interact with the child’s perceptual abilities to shape the learning experience.
Cranial ontogeny of Thamnophis radix (Serpentes: Colubroidea) with a re-evaluation of current paradigms of snake skull evolution

Accurate knowledge of skeletal ontogeny in extant organisms is crucial in understanding important morpho-functional systems and in enabling inferences of the ontogenetic stage of fossil specimens. However, detailed knowledge of skeletal ontogeny is lacking for most squamates, including snakes. Very few studies have discussed postnatal development in snakes, with none incorporating data from all three major ontogenetic stages—embryonic, juvenile and adult. Here, we provide the first analysis encompassing these three ontogenetic stages for any squamate, using the first complete micro-computed tomography (micro-CT)-based segmentations of any non-adult snake, based on fresh specimens of Thamnophis radix. The most significant ontogenetic changes involve the feeding apparatus, with major elongation of the tooth-bearing elements and jaw suspensorium causing a posterior shift in the jaw articulation. This shift enables macrostomy (large-gaped feeding in snakes) and occurs in T. radix via a different developmental trajectory than in most other macrostomatans, indicating that the evolution of macrostomy is more complex than previously thought. The braincase of T. radix is also evolutionarily unique among derived snakes in lacking a crista circumfenestralis, a phenomenon considered herein to represent paedomorphic retention of the embryonic condition. We thus present numerous important challenges to current paradigms regarding snake cranial evolution.
Optimal foraging and the information theory of gambling

Part of the life cycle of an ant colony is simple: a colony collects resources; these resources are converted into more ants, and these ants in turn collect more resources. Because more ants collect more resources, this is a multiplicative process, and the expected logarithm of the amount of resources (equivalently, geometric mean (Dempster, 1955; MacArthur, 1965)) determines how successful the colony will be in the long run. Over 60 years ago, Kelly (1956) showed, using information theoretic techniques, that the rate of growth of resources for such a situation is optimised by probability matching. Thus, in the case of ants the fraction of the colony foraging at a given location should be proportional to the probability that resources will be found there, a result widely applied in the mathematics of gambling. This theoretical optimum generates predictions for which collective ant movement strategies might have evolved. In this second of three papers, we show how colony level optimal foraging behaviour can be achieved by mapping movement to Markov chain Monte Carlo methods, specifically Hamiltonian Markov chain Monte Carlo (HMC). This can be done by the ants following a (noisy) local measurement of the (logarithm of) the resource probability gradient (possibly supplemented with momentum, i.e. a propensity to move in the same direction). This maps the problem of foraging (via the information theory of gambling, stochastic dynamics and techniques employed within Bayesian statistics to efficiently sample from probability distributions) to simple models of ant foraging behaviour. This identification has broad applicability, facilitates the application of information theory approaches to understanding animal cognition, and unifies insights from existing biomechanical, cognitive, random and optimality movement paradigms. At the cost of requiring ants to obtain (noisy) resource gradient information, we show that this model is both efficient, and matches a number of characteristics of real ant exploration.
Infection of Dendritic Cells With Mycobacterium avium subspecies hominissuis Exhibits a Functionally Tolerogenic Phenotype in Response to Toll-Like Receptor Agonists via IL-10/Cox2/PGE2/EP2 Axis

Mycobacterium avium subspecies hominissuis (MAH) is the most common agent causing nontuberculous mycobacterial disease in humans. It mainly causes chronic and slowly progressive pulmonary disease (PD), which requires a long-term treatment and allows opportunistic co-infection by common pulmonary pathogens such as Pseudomonas aeruginosa, Staphylococcus aureus, and Aspergillus spp. , thereby resulting in alteration of host immune response. In the present study, we investigated the phenotypical and functional alterations of dendritic cells (DCs), a bridge antigen-presenting cell between innate and adaptive immunity, following MAH infection in response to various toll-like receptor (TLR) agonists mimicking co-infection conditions, along with subsequent T cell response. Interestingly, MAH-infected DCs produced interleukin (IL)-10 significantly and decreased the level of IL-12p70 in response to Poly I:C and LPS, although not so in response to Pam3CSK4, imiquimod, or CpG oligodeoxynucleotide, thereby indicating that the TLR3 and TLR4 agonists functionally altered MAH-infected DCs toward a tolerogenic phenotype. Moreover, IL-10-producing tolerogenic DCs were remarkably induced by MAH and P. aeruginosa co-infection. To precisely elucidate how these TLR agonists induce tolerogenic DCs upon MAH infection, we sought to clarify the major mechanisms involved, using LPS, which caused the greatest increase in IL-10 production by the TLR agonists. Increased IL-10 stimulated the creation of tolerogenic DCs by significantly reducing MHC class II expression and MHC class II-antigen presentation, eventually inhibiting CD4+ T cell proliferation, along with decreased IFN-γ and IL-2. The tolerogenic phenotypes of MAH/LPS-treated DCs were restored by anti-IL-10 neutralization, validating the induction of tolerogenicity by IL-10. Interestingly, IL-10-producing-tolerogenic DCs were observed after infection with live MAH, rather than with inactivated or dead MAH. In addition, TLR2−/− and TLR4−/− DCs confirmed the association of IL-10 production with TLR2 and TLR4 signaling; IL-10 production synergistically increased when both TLR4 and TLR2 were involved. Expression of Cox2 and PGE2 increased along with IL-10 while that of IL-10 was inhibited by their selective inhibitors celecoxib and anti-EP2 antibody, respectively. Thus, the tolerogenic phenotypes of MAH/LPS-treated DCs were proven to be induced by Cox-2/PGE2-dependent EP2 signaling as the main mechanism. These findings may provide important clues that the tolerogenic cascade in MAH-infected DCs induced by TLR 4 signaling can alter host immune response.
Drawing a Link Between Genetic Inheritance and Meiosis: A Set of Exercises for the Undergraduate Biology Classroom†

Alleles are passed from parent to offspring through meiotic cell division and subsequent fusion of gametes. Despite this important link, general biology courses at the high school and college levels frequently discuss meiosis and genetic inheritance as two distinct content areas. As a consequence, students may leave biology courses with a working knowledge of both meiosis and genetic inheritance in isolation rather than understanding them as interconnected topics. In this paper, we describe and provide a series of classroom exercises that prompt students to explore the connection between meiosis and genetic inheritance. Specifically, students draw cells containing chromosomes with labeled alleles to illustrate key steps in the formation of gametes during meiosis and the subsequent fusion of gametes during fertilization. We believe that this approach is appropriate for either group or individual work, during or outside of class time, and we describe potential benefits for students and instructors.
The Emergence of Spindles and K-Complexes and the Role of the Dorsal Caudal Part of the Anterior Cingulate as the Generator of K-Complexes

The large multicomponent K-complex (KC) and the rhythmic spindle are the hallmarks of non-rapid eye movement (NREM)-2 sleep stage. We studied with magnetoencephalography (MEG) the progress of light sleep (NREM-1 and NREM-2) and emergence of KCs and spindles. Seven periods of interest (POI) were analyzed: wakefulness, the two quiet “core” periods of light sleep (periods free from any prominent phasic or oscillatory events) and four periods before and during spindles and KCs. For each POI, eight 2-s (1250 time slices) segments were used. We employed magnetic field tomography (MFT) to extract an independent tomographic estimate of brain activity from each MEG data sample. The spectral power was then computed for each voxel in the brain for each segment of each POI. The sets of eight maps from two POIs were contrasted using a voxel-by-voxel t-test. Only increased spectral power was identified in the four key contrasts between POIs before and during spindles and KCs versus the NREM2 core. Common increases were identified for all four subjects, especially within and close to the anterior cingulate cortex (ACC). These common increases were widespread for low frequencies, while for higher frequencies they were focal, confined to specific brain areas. For the pre-KC POI, only one prominent increase was identified, confined to the theta/alpha bands in a small area in the dorsal caudal part of ACC (dcACC). During KCs, the activity in this area grows in intensity and extent (in space and frequency), filling the space between the areas that expanded their low frequency activity (in the delta band) during NREM2 compared to NREM1. Our main finding is that prominent spectral power increases before NREM2 graphoelements are confined to the dcACC, and only for KCs, sharing common features with changes of activity in dcACC of the well-studied error related negativity (ERN). ERN is seen in awake state, in perceptual conflict and situations where there is a difference between expected and actual environmental or internal events. These results suggest that a KC is the sleep side of the awake state ERN, both serving their putative sentinel roles in the frame of the saliency network.
The Effects of Leptin on Glial Cells in Neurological Diseases

It is known that various endocrine modulators, including leptin and ghrelin, have neuroprotective roles in neurological diseases. Leptin is a hormone produced by adipocytes and was originally identified as a gene related to obesity in mice. The leptin receptors in the hypothalamus are the main target for the homeostatic regulation of body weight. Recent studies have demonstrated that leptin receptors are also expressed in other regions of the central nervous system (CNS), such as the hippocampus, cerebral cortex, and spinal cord. Accordingly, these studies identified the involvement of leptin in the regulation of neuronal survival and neural development. Furthermore, leptin has been shown to have neuroprotective functions in animal models of neurological diseases and demyelination. These observations also suggest that dysregulation of leptin signaling may be involved in the association between neurodegeneration and obesity. In this review, we summarize novel functions of leptin in animal models of neurodegenerative diseases. Specifically, we focus on the emerging evidence for the role of leptin in non-neuronal cells in the CNS, including astrocytes, microglia, and oligodendrocytes. Understanding leptin-mediated neuroprotective signals and molecular mechanisms underlying remyelination will be helpful to establish therapeutic strategies against neurological diseases.
Rap GTPase Interactor: A Potential Marker for Cancer Prognosis Following Kidney Transplantation

Post-transplant (post-Tx) kidney cancer has become the second-highest cause of death in kidney recipients. Late diagnosis and treatment are the main reasons for high mortality. Further research into early diagnosis and potential treatment is therefore required. In this current study, through genome-wide RNA-Seq profile analysis of post-Tx malignant blood samples and post-Tx non-malignant control blood samples (CTRL-Tx), we found Rap GTPase Interactor (RADIL) and Aprataxin (APTX) to be the most meaningful markers for cancer diagnosis. Receiver operating characteristic (ROC) curve analysis showed that the area under the curve (AUC) of the RADIL-APTX signature model was 0.92 (P < 0.0001). Similarly, the AUC of RADIL alone was 0.91 (P < 0.0001) and that of APTX was 0.81 (P = 0.001). Additionally, using a semi-supervised method, we found that RADIL alone could better predict malignancies in kidney transplantation recipients than APTX alone. Kaplan-Meier analysis indicated that RADIL was expressed significantly higher in the early stages (I and II) of kidney, liver, stomach, and pancreatic cancer, suggesting the potential use of RADIL in early diagnosis. Multivariable Cox regression analysis found that RADIL together with other factors (including age, stage III, stage IV and CD8+ T cells) play a key role in kidney cancer development. Among those factors, RADIL could promote kidney cancer development (HR > 1, P < 0.05) while CD8+ T cells could inhibit kidney cancer development (HR < 1, P < 0.05). RADIL may be a new immunotherapy target for kidney cancer post kidney transplantation.
Invariant NKT Cell-Mediated Modulation of ILC1s as a Tool for Mucosal Immune Intervention

Non-NK group 1 innate lymphoid cells (ILC1s), mainly investigated in the mucosal areas of the intestine, are well-known to contribute to anti-parasitic and anti-bacterial immune responses. Recently, our group revealed that lung ILC1s become activated during murine influenza infection, thereby contributing to viral clearance. In this context, worldwide seasonal influenza infections often result in severe disease outbreaks leading to high morbidity and mortality. Therefore, new immune interventions are urgently needed. In contrast to NK cells, the potential of non-NK ILC1s to become functionally tailored by immune modulators to contribute to the combat against mucosal-transmitted viral pathogens has not yet been addressed. The present study aimed at assessing the potential of ILC1s to become modulated by iNKT cells activated through the CD1d agonist αGalCerMPEG. Our results demonstrate an improved functional responsiveness of murine lung and splenic ILC1s following iNKT cell stimulation by the mucosal route, as demonstrated by enhanced surface expression of TNF-related apoptosis-inducing ligand (TRAIL), CD49a and CD28, and increased secretion of IFNγ. Interestingly, iNKT cell stimulation also induced the expression of the immune checkpoint molecules GITR and CTLA-4, which represent crucial points of action for immune regulation. An in vivo influenza infection model revealed that intranasal activation of ILC1s by αGalCerMPEG contributed to increased viral clearance as shown by reduced viral loads in the lungs. The findings that ILC1s can become modulated by mucosally activated iNKT cells in a beneficial manner emphasize their up to now underestimated potential and renders them to be considered as targets for novel immune interventions.