Miracle-dz/UniFAR-FTUs huggingface dataset:
The effects of local homogeneity assumptions in metapopulation models of infectious disease

Computational models of infectious disease can be broadly categorized into two types: individual-based (agent-based) or compartmental models. While there are clear conceptual distinctions between these methodologies, a fair comparison of the approaches is difficult to achieve. Here, we carry out such a comparison by building a set of compartmental metapopulation models from an agent-based representation of a real population. By adjusting the compartmental model to approximately match the dynamics of the agent-based model, we identify two key qualitative properties of the individual-based dynamics which are lost upon aggregation into metapopulations. These are (i) the local depletion of susceptibility to infection and (ii) decoupling of different regional groups due to correlation between commuting behaviours and contact rates. The first of these effects is a general consequence of aggregating small, closely connected groups (i.e. families) into larger homogeneous metapopulations. The second can be interpreted as a consequence of aggregating two distinct types of individuals: school children, who travel short distances but have many potentially infectious contacts, and adults, who travel further but tend to have fewer contacts capable of transmitting infection. Our results could be generalized to other types of correlations between the characteristics of individuals and the behaviours that distinguish them.
Public consultation in the evaluation of animal research protocols

One response to calls for increased openness in animal research is to make protocols publicly accessible, but it is unclear what type of input the public would provide if given this opportunity. In this study we invited public responses to five different research projects, using non-technical summaries intended for lay audiences. Our aim was to assess the potential for this type of public consultation in protocol review, and a secondary aim was to better understand what types of animal research people are willing to accept and why. US participants (n = 1521) were asked (via an online survey) “Do you support the use of these (insert species) for this research”, and responded using a seven-point scale (1 = “No”, 4 = “Neutral”, and 7 = “Yes”). Participants were asked to explain the reasons for their choice; open-ended text responses were subjected to thematic analysis. Most participants (89.7%) provided clear comments, showing the potential of an online forum to elicit feedback. Four themes were prevalent in participant reasoning regarding their support for the proposed research: 1) impact on animals, 2) impact on humans, 3) scientific merit, and 4) availability of alternatives. Participant support for the proposed research varied but on average was close to neutral (mean ± SD: 4.5 ± 2.19) suggesting some ambivalence to this animal use. The protocol describing Parkinson’s research (on monkeys) was least supported (3.9 ± 2.17) and the transplant research (on pigs) was most supported (4.9 ± 2.02). These results indicate that public participants are sensitive to specifics of a protocol. We conclude that an online forum can provide meaningful public input on proposed animal research, offering research institutions the opportunity for improved transparency and the chance to reduce the risk that they engage in studies that are out of step with community values.
The AGN fuelling/feedback cycle in nearby radio galaxies - IV. Molecular gas conditions and jet-ISM interaction in NGC 3100

This is the fourth paper of a series investigating the AGN fuelling/feedback processes in a sample of eleven nearby low-excitation radio galaxies (LERGs). In this paper we present follow-up Atacama Large Millimeter/submillimeter Array (ALMA) observations of one source, NGC 3100, targeting the 12CO(1-0), 12CO(3-2), HCO+(4-3), SiO(3-2) and HNCO(6-5) molecular transitions. 12CO(1-0) and 12CO(3-2) lines are nicely detected and complement our previous 12CO(2-1) data. By comparing the relative strength of these three CO transitions, we find extreme gas excitation conditions (i.e. Tex ≳ 50 K) in regions that are spatially correlated with the radio lobes, supporting the case for a jet-ISM interaction. An accurate study of the CO kinematics demonstrates that, although the bulk of the gas is regularly rotating, two distinct non-rotational kinematic components can be identified in the inner gas regions: one can be associated to inflow/outflow streaming motions induced by a two-armed spiral perturbation; the second one is consistent with a jet-induced outflow with vmax ≈ 200 km s−1 and $\dot{M}\lesssim 0.12$ M⊙ yr−1. These values indicate that the jet-CO coupling ongoing in NGC 3100 is only mildly affecting the gas kinematics, as opposed to what expected from existing simulations and other observational studies of (sub-)kpc scale jet-cold gas interactions. HCO+(4-3) emission is tentatively detected in a small area adjacent to the base of the northern radio lobe, possibly tracing a region of jet-induced gas compression. The SiO(3-2) and HNCO(6-5) shock tracers are undetected: this - along with the tentative HCO+(4-3) detection - may be consistent with a deficiency of very dense (i.e. ncrit > 106 cm−3) cold gas in the central regions of NGC 3100.
Finding Cortical Subregions Regarding the Dorsal Language Pathway Based on the Structural Connectivity

Although the language-related fiber pathways in the human brain, such as the superior longitudinal fasciculus (SLF) and arcuate fasciculus (AF), are already well-known, understanding more sophisticated cortical regions connected by the fiber tracts is essential to scrutinize the structural connectivity of language circuits. With the regions of interest that were selected based on the Brainnetome atlas, the fiber orientation distribution estimation method for tractography was used to produce further elaborate connectivity information. The results indicated that both fiber bundles had two distinct connections with the prefrontal cortex (PFC). The SLF-II and dorsal AF are mainly connected to the rostrodorsal part of the inferior parietal cortex (IPC) and lateral part of the fusiform gyrus with the inferior frontal junction (IFJ), respectively. In contrast, the SLF-III and ventral AF were primarily linked to the anterior part of the supramarginal gyrus and superior part of the temporal cortex with the inferior frontal cortex, including the Broca's area. Moreover, the IFJ in the PFC, which has rarely been emphasized as a language-related subregion, also had the strongest connectivity with the previously known language-related subregions among the PFC; consequently, we proposed that these specific regions are interconnected via the SLF and AF within the PFC, IPC, and temporal cortex as language-related circuitry.
The diagonal coinvariant ring of a complex reflection group

For an irreducible complex reflection group $W$ of rank $n$ containing $N$ reflections, we put $g=2N/n$ and construct a $(g+1)^n$-dimensional irreducible representation of the Cherednik algebra which is (as a vector space) a quotient of the diagonal coinvariant ring of $W$. We propose that this representation of the Cherednik algebra is the single largest representation bearing this relationship to the diagonal coinvariant ring, and that further corrections to this estimate of the dimension of the diagonal coinvariant ring by $(g+1)^n$ should be orders of magnitude smaller. A crucial ingredient in the construction is the existence of a dot action of a certain product of symmetric groups acting on the parameter space of the rational Cherednik algebra and leaving invariant both the finite Hecke algebra and the spherical subalgebra; this fact is a consequence of ideas of Berest-Chalykh on the relationship between the Cherednik algebra and quasi-invariants.
Developmental features of the canid proximocaudal femur

We continued direct morphological studies of the canid coxofemoral joint, considering early‐life spatial relationships around the locus of the proximocaudal joint capsule insertion. Our primary goal was to elucidate the postnatal developmental gross anatomy of the proximocaudal femur, among juveniles across Canidae. From an original database of 267 independent (museum) specimens from 11 canid taxa and 1 hybrid taxon, we identified 29 ancient or modern candidate juvenile specimens (nine taxa and one hybrid taxon). Based on optimal ability to recognize landmarks, the best photographic data were categorized into five groups of four each (n = 20). The data groups approximated early juvenile, early‐mid juvenile, mid‐juvenile, mid‐late juvenile; and young adult stages. In this descriptive photographic essay, we demonstrate the developmental spatial proximity among (a) the dorsal meeting of the respective lateral and medial extensions from the growth centers of the femoral head and greater trochanter; (b) the caudodorsal aspect of the coxofemoral joint capsule attachment; (c) a segment of the proximocaudal femoral shaft physis; and (d) an eventual associated mineralized prominence. The latter occurs frequently but not universally, suggesting natural population variability across taxa. Across taxa and juvenile age categories, the morphology thus supports developmental conservation among ancient and modern Canidae. The biomechanical and biological cause‐effect implications are not yet clear. For zoological purposes, we apply the term postdevelopmental mineralized prominence to the residual caudolateral surface feature. We extend the original anatomical work of Morgan in zoological and phylogenic arenas, using direct observation of cleared skeletal specimens.
Counter‐Rotating Type Pump Unit (Rotational Behaviors)

Turbo‐pumps have weak points, such as the pumping operation becomes unstable in the rising portion of the head characteristics and/or the cavitation occurs at the low suction head. To overcome simultaneously both weak points, the authors invented the unique pump unit composed of the tandem impellers and the counter‐rotating type motor with the double rotational armatures. The front and the rear impellers are driven by the inner and the outer armatures of the motor, respectively. Both impeller speeds are automatically and smartly adjusted in response to the pumping discharge. Such speeds controlled smartly contribute pretty well to suppress not only the unstable performances at the low discharge but also the cavitation at the high discharge, as verified in the previous paper.Continuously, the effects of the impeller profiles not only on the pump performances but also on the rotational behaviors are discussed in this paper. Two kinds of the blade profile, giving the lower and the higher heads, were prepared as the front and the rear impellers. The pump performances and the both impeller speeds are affected undoubtedly by not only the discharge but also the impeller profiles. The rotational speed of the front impeller is faster than the speed of the rear impeller in the wide discharge, while the tandem impellers composed of the front impeller giving the lower head and the rear impeller giving the higher head. Such behaviors are caused by making the angular momentum change through the front impeller coincide with that through the rear impeller.Turbo‐pumps have weak points, such as the pumping operation becomes unstable in the rising portion of the head characteristics and/or the cavitation occurs at the low suction head. To overcome simultaneously both weak points, the authors invented the unique pump unit composed of the tandem impellers and the counter‐rotating type motor with the double rotational armatures. The front and the rear impellers are driven by the inner and the outer armatures of the motor, respectively. Both impeller speeds are automatically and smartly adjusted in response to the pumping discharge. Such speeds controlled smartly contribute pretty well to suppress not only the unstable performances at the low discharge but also the cavitation at the high discharge, as verified in the previous paper.Continuously, the effects of the impeller profiles not only on the pump performances but also on the rotational behaviors are discussed in this paper. Two kinds of the blade profile, giving the lower and the higher heads, were prepared.
Selective prediction‐set models with coverage rate guarantees

The current approach to using machine learning (ML) algorithms in healthcare is to either require clinician oversight for every use case or use their predictions without any human oversight. We explore a middle ground that lets ML algorithms abstain from making a prediction to simultaneously improve their reliability and reduce the burden placed on human experts. To this end, we present a general penalized loss minimization framework for training selective prediction‐set (SPS) models, which choose to either output a prediction set or abstain. The resulting models abstain when the outcome is difficult to predict accurately, such as on subjects who are too different from the training data, and achieve higher accuracy on those they do give predictions for. We then introduce a model‐agnostic, statistical inference procedure for the coverage rate of an SPS model that ensembles individual models trained using K‐fold cross‐validation. We find that SPS ensembles attain prediction‐set coverage rates closer to the nominal level and have narrower confidence intervals for its marginal coverage rate. We apply our method to train neural networks that abstain more for out‐of‐sample images on the MNIST digit prediction task and achieve higher predictive accuracy for ICU patients compared to existing approaches.
Improved Diagnosis of Viable Parenchymal Neurocysticercosis by Combining Antibody Banding Patterns on Enzyme-Linked Immunoelectrotransfer Blot (EITB) with Antigen Enzyme-Linked Immunosorbent Assay (ELISA)

The diagnosis of neuricysticercosis (NCC) depends on neuroimaging and serological confirmation. While antibody detection by enzyme-linked immunoelectrotransfer blot (EITB) fails to predict viable NCC, EITB banding patterns provide information about the host’s infection course. Adding antigen enzyme-linked immunosorbent assay (Ag-ELISA) results to EITB banding patterns may improve their ability to predict or rule out of viable NCC. ABSTRACT The diagnosis of neurocysticercosis (NCC) depends on neuroimaging and serological confirmation. While antibody detection by enzyme-linked immunoelectrotransfer blot (EITB) fails to predict viable NCC, EITB banding patterns provide information about the host’s infection course. Adding antigen enzyme-linked immunosorbent assay (Ag-ELISA) results to EITB banding patterns may improve their ability to predict or rule out of viable NCC. We assessed whether combining EITB banding patterns with Ag-ELISA improves discrimination of viable infection in imaging-confirmed parenchymal NCC. EITB banding patterns were grouped into classes using latent class analysis. True-positive and false-negative Ag-ELISA results in each class were compared using Fisher’s exact test. Four classes were identified: 1, EITB negative or positive to GP50 alone (GP50 antigen family); 2, positive to GP42-39 and GP24 (T24/42 family), with or without GP50; and 3 and 4, positive to GP50, GP42-39, and GP24 and reacting to bands in the 8-kDa family. Most cases in classes 3 and 4 had viable NCC (82% and 88%, respectively) compared to classes 2 and 1 (53% and 5%, respectively). Adding positive Ag-ELISA results to class 2 predicted all viable NCC cases (22/22 [100%]), whereas 11/40 patients (27.5%) Ag-ELISA negative had viable NCC (P < 0.001). Only 1/4 patients (25%) Ag-ELISA positive in class 1 had viable NCC, whereas 1/36 patients (2.8%) Ag-ELISA negative had viable NCC (P = 0.192). In classes 3 and 4, adding Ag-ELISA was not contributory. Combining Ag-ELISA with EITB banding patterns improves discrimination of viable from nonviable NCC, particularly for class 2 responses. Together, these complement neuroimaging more appropriately for the diagnosis of viable NCC.
Development of a finite element lumbar spine model to predict intervertebral disc herniation risk factors

Abstract The objective of the current study was to develop a lumbar motion segment FE model that predicts disc herniation risk. The posterolateral nucleus extrusion force and disc pressure increased as the amount of flexion and magnitude of compression was increased in all loading scenarios. The nucleus extrusion force and posterior stress in the annulus both increased when exposed to a combination of compression and flexion. Results of the current study confirmed the authors hypothesis that the model would accurately predict herniation risk when exposed to a biomechanical environment known to cause herniations.
Oral health coverage in the Family Health Strategy and use of dental services in adolescents in Mato Grosso do Sul, Brazil, 2019: cross-sectional study*

Objective: To analyze the association between the coverage by oral health teams in the Family Health Strategy (FHS-OH) and the use of dental services among 12-year-old adolescents in the state of Mato Grosso do Sul, Brazil, 2019. Methods: This is a cross-sectional study involving school-based research, which adopted the use of dental services as its outcome. Structural equation modeling was used to test the association between covariates and the outcome. Results: Of the 615 participants, 74.0% used dental services in the last three years. ESF-SB (oral health coverage by family health strategy, acronym in Portuguese) ≥50% was associated with a greater use of public dental services [standardized coefficient (SC) = 0.10 -95%CI 0.01;0.18], a lower use of these services for prevention (SC = -0.07 -95%CI -0.17;0.01) and higher unhealthy food consumption (SC = 0.19 -95%CI 0.11;0.26). Conclusion: Higher ESF-SB coverage was associated with a lower use of dental services for prevention and higher unhealthy food consumption. Teams must organize the access to oral health service and qualify the work process.
Mucin1 relieves acute lung injury by inhibiting inflammation and oxidative stress

Acute lung injury/acute respiratory distress syndrome (ALI/ARDS) is a kind of diffuse inflammatory injury caused by various factors, characterized by respiratory distress and progressive hypoxemia. It is a common clinical critical illness. The aim of this study was to investigate the effect and mechanism of the Mucin1 (MUC1) gene and its recombinant protein on lipopolysaccharide (LPS)-induced ALI/ARDS. We cultured human alveolar epithelial cell line (BEAS-2B) and used MUC1 overexpression lentivirus to detect the effect of MUC1 gene on BEAS-2B cells. In addition, we used LPS to induce ALI/ARDS in C57/BL6 mice and use hematoxylin and eosin (H&E) staining to verify the effect of their modeling. Recombinant MUC1 protein was injected subcutaneously into mice. We examined the effect of MUC1 on ALI/ARDS in mice by detecting the expression of inflammatory factors and oxidative stress molecules in mouse lung tissue, bronchoalveolar lavage fluid (BALF) and serum. Overexpression of MUC1 effectively ameliorated LPS-induced damage to BEAS-2B cells. Results of H&E staining indicate that LPS successfully induced ALI/ARDS in mice and MUC1 attenuated lung injury. MUC1 also reduced the expression of inflammatory factors (IL-1β, TNF-α, IL-6 and IL-8) and oxidative stress levels in mice. In addition, LPS results in an increase in the activity of the TLR4/NF-κB signaling pathway in mice, whereas MUC1 decreased the expression of the TLR4/NF-κB signaling pathway. MUC1 inhibited the activity of TLR4/NF-κB signaling pathway and reduced the level of inflammation and oxidative stress in lung tissue of ALI mice.
Structural Basis of Pore Formation in the Mannose Phosphotransferase System by Pediocin PA-1

Listeria monocytogenes is a ubiquitous microorganism responsible for listeriosis, a rare but severe disease in humans, who become infected by ingesting contaminated food products (i.e., dairy, meat, fish, and vegetables): the disease has a fatality rate of 33%. Pediocin PA-1 is an important commercial additive used in food production to inhibit Listeria species. ABSTRACT Bacteriocins are ribosomally synthesized bacterial antimicrobial peptides that have a narrow spectrum of antibacterial activity against species closely related to the producers. Pediocin-like (or class IIa) bacteriocins (PLBs) exhibit antibacterial activity against several Gram-positive bacterial strains by forming pores in the cytoplasmic membrane of target cells with a specific receptor, the mannose phosphotransferase system (man-PTS). In this study, we report the cryo-electron microscopy structures of man-PTS from Listeria monocytogenes alone and its complex with pediocin PA-1, the first and most extensively studied representative PLB, at resolutions of 3.12 and 2.45 Å, respectively. The structures revealed that the binding of pediocin PA-1 opens the Core domain of man-PTS away from its Vmotif domain, creating a pore through the cytoplasmic membranes of target cells. During this process, the N-terminal β-sheet region of pediocin PA-1 can specifically attach to the extracellular surface of the man-PTS Core domain, whereas the C-terminal half penetrates the membrane and cracks the man-PTS like a wedge. Thus, our findings shed light on a design of novel PLBs that can kill the target pathogenic bacteria. IMPORTANCE Listeria monocytogenes is a ubiquitous microorganism responsible for listeriosis, a rare but severe disease in humans, who become infected by ingesting contaminated food products (i.e., dairy, meat, fish, and vegetables): the disease has a fatality rate of 33%. Pediocin PA-1 is an important commercial additive used in food production to inhibit Listeria species. The mannose phosphotransferase system (man-PTS) is responsible for the sensitivity of Listeria monocytogenes to pediocin PA-1. In this study, we report the cryo-EM structures of man-PTS from Listeria monocytogenes alone and its complex with pediocin PA-1 at resolutions of 3.12 and 2.45 Å, respectively. Our results facilitate the understanding of the mode of action of class IIa bacteriocins as an alternative to antibiotics.
Unsafe Sharps Disposal Among Insulin-Using Patients With Diabetes Mellitus: An Emerging Global Crisis

Approximately eight billion therapeutic injections are administered outside of medical treatment facilities annually. The management of diabetes mellitus (DM) includes self-monitoring of blood glucose levels and administration of insulin and injectable non–insulin-related medications. The lancets, needles, and syringes used for DM management are categorized as medical sharps. Improperly discarded medical sharps can cause needlestick injuries in unsuspecting individuals and thereby pose a considerable public health risk. Release of these items into the environment will likely increase with the rising worldwide prevalence of DM, and a public safety crisis will emerge if proper disposal measures are not emphasized. This article reviews the literature from various geopolitical regions and describes how a substantial number of patients with DM improperly discard their sharps. Data support the need to develop multifaceted and innovative approaches to reduce risk associated with improper disposal of DM-related medical sharps into local communities.