Miracle-dz/UniFAR-FTUs huggingface dataset:
Prion Strain Differences in Accumulation of PrPSc on Neurons and Glia Are Associated with Similar Expression Profiles of Neuroinflammatory Genes: Comparison of Three Prion Strains

Misfolding and aggregation of host proteins are important features of the pathogenesis of neurodegenerative diseases including Alzheimer’s disease, Parkinson’s disease, frontotemporal dementia and prion diseases. In all these diseases, the misfolded protein increases in amount by a mechanism involving seeded polymerization. In prion diseases, host prion protein is misfolded to form a pathogenic protease-resistant form, PrPSc, which accumulates in neurons, astroglia and microglia in the CNS. Here using dual-staining immunohistochemistry, we compared the cell specificity of PrPSc accumulation at early preclinical times post-infection using three mouse scrapie strains that differ in brain regional pathology. PrPSc from each strain had a different pattern of cell specificity. Strain 22L was mainly associated with astroglia, whereas strain ME7 was mainly associated with neurons and neuropil. In thalamus and cortex, strain RML was similar to 22L, but in substantia nigra, RML was similar to ME7. Expression of 90 genes involved in neuroinflammation was studied quantitatively using mRNA from thalamus at preclinical times. Surprisingly, despite the cellular differences in PrPSc accumulation, the pattern of upregulated genes was similar for all three strains, and the small differences observed correlated with variations in the early disease tempo. Gene upregulation correlated with activation of both astroglia and microglia detected in early disease prior to vacuolar pathology or clinical signs. Interestingly, the profile of upregulated genes in scrapie differed markedly from that seen in two acute viral CNS diseases (LaCrosse virus and BE polytropic Friend retrovirus) that had reactive gliosis at levels similar to our prion-infected mice.
Viral infection of the thymus

We have examined infection of the thymus during congenitally acquired chronic lymphocytic choriomeningitis virus (LCMV) infection of mice, a classic model of antigen-specific T-cell tolerance. Our results show that (i) infection starts at the fetal stage and is maintained throughout adulthood, and (ii) this chronic infection of the thymus can be eliminated by transfer of virus-specific cytotoxic T lymphocytes (CTL) that infiltrate the thymus and clear all viral products from both medullary and cortical regions. Elimination of virus from the thymus results in abrogation of tolerance. During the fetal stage, the predominant cell type infected is the earliest precursor of T cells with a surface phenotype of Thy1+ CD4- CD8- J11d+. In the adult thymus, infection is confined primarily to the cortisone-resistant thymocytes present in the medullary region. The infected cells are CD4+ and J11d+. The presence of J11d, a marker usually associated with immature thymocytes, on infected single positive CD4+ "mature" thymocytes is intriguing and suggests that infection by this noncytolytic virus may affect development of T cells. There is minimal infection of the CD8+ medullary thymocytes or of the double positive (CD4+ CD8+) cells present in the cortex. Infection within the cortex is confined to the stromal cells. Interestingly, there is infection of the double negative (CD4- CD8-) thymocytes in the adult thymus, showing that even during adulthood the newly developing T cells are susceptible to infection by LCMV. Virus can be eliminated from the thymuses of these carrier mice by adoptive transfer of medullary region first and then from the thymic cortex. This result clearly shows the need to reevaluate the widely held notion that mature T cells are unable to reenter the thymus. In fact, in our experiments the donor T cells made up to 20 to 30% of the total cells in the thymus at 5 to 7 days after the transfer. The number of donor T cells declined as virus was eliminated from the thymus, and at 1 month posttransfer, the donor T cells were hardly detectable. The results of this study examining the dynamics of viral infection and clearance from the thymus, the primary site of T-cell development, have implications for understanding tolerance induction in chronic viral infections.
BurnMan: A lower mantle mineral physics toolkit

We present BurnMan, an open‐source mineral physics toolbox to determine elastic properties for specified compositions in the lower mantle by solving an Equation of State (EoS). The toolbox, written in Python, can be used to evaluate seismic velocities of new mineral physics data or geodynamic models, and as the forward model in inversions for mantle composition. The user can define the composition from a list of minerals provided for the lower mantle or easily include their own. BurnMan provides choices in methodology, both for the EoS and for the multiphase averaging scheme. The results can be visually or quantitatively compared to observed seismic models. Example user scripts show how to go through these steps. This paper includes several examples realized with BurnMan: First, we benchmark the computations to check for correctness. Second, we exemplify two pitfalls in EoS modeling: using a different EoS than the one used to derive the mineral physical parameters or using an incorrect averaging scheme. Both pitfalls have led to incorrect conclusions on lower mantle composition and temperature in the literature. We further illustrate that fitting elastic velocities separately or jointly leads to different Mg/Si ratios for the lower mantle. However, we find that, within mineral physical uncertainties, a pyrolitic composition can match PREM very well. Finally, we find that uncertainties on specific input parameters result in a considerable amount of variation in both magnitude and gradient of the seismic velocities.
Periodic Variability in the Large-Scale Southern Hemisphere Atmospheric Circulation

Predictable Behavior Few internally forced large-scale atmospheric circulation patterns exhibit periodic behavior, and those that do are centered in the tropics. Identifying these periodic processes is important for understanding the dynamics of weather. Thompson and Barnes (p. 641) report the discovery of a 20- to 30-day periodicity in the atmospheric circulation in the Southern Hemisphere. The oscillation could potentially drive large-scale climate variability throughout much of the mid-latitude Southern Hemisphere. Large-scale atmospheric circulation in the Southern Hemisphere oscillates on a time scale of roughly 20 to 30 days. Periodic behavior in the climate system has important implications not only for weather prediction but also for understanding and interpreting the physical processes that drive climate variability. Here we demonstrate that the large-scale Southern Hemisphere atmospheric circulation exhibits marked periodicity on time scales of approximately 20 to 30 days. The periodicity is tied to the Southern Hemisphere baroclinic annular mode and emerges in hemispheric-scale averages of the eddy fluxes of heat, the eddy kinetic energy, and precipitation. Observational and theoretical analyses suggest that the oscillation results from feedbacks between the extratropical baroclinicity, the wave fluxes of heat, and radiative damping. The oscillation plays a potentially profound role in driving large-scale climate variability throughout much of the mid-latitude Southern Hemisphere.
How many bits does it take for a stimulus to be salient?

Visual saliency has been shown to depend on the unpredictability of the visual stimulus given its surround. Various previous works have advocated the equivalence between stimulus saliency and uncompressibility. We propose a direct measure of this quantity, namely the number of bits required by an optimal video compressor to encode a given video patch, and show that features derived from this measure are highly predictive of eye fixations. To account for global saliency effects, these are embedded in a Markov random field model. The resulting saliency measure is shown to achieve state-of-the-art accuracy for the prediction of fixations, at a very low computational cost. Since most modern cameras incorporate video encoders, this paves the way for in-camera saliency estimation, which could be useful in a variety of computer vision applications.
Pseudomonas fluorescens and Trichoderma asperellum Enhance Expression of Gα Subunits of the Pea Heterotrimeric G-protein during Erysiphe pisi Infection

We investigated the transcript accumulation patterns of all three subunits of heterotrimeric G-proteins (Gα1 and 2, Gβ, and Gγ) in pea under stimulation of two soil-inhabiting rhizosphere microbes Pseudomonas fluorescens OKC and Trichoderma asperellum T42. The microbes were either applied individually or co-inoculated and the transcript accumulation patterns were also investigated after challenging the same plants with a fungal biotrophic pathogen Erysiphe pisi. We observed that mostly the transcripts of Gα 1 and 2 subunits were accumulated when the plants were treated with the microbes (OKC and T42) either individually or co-inoculated. However, transcript accumulations of Gα subunits were highest in the T42 treatment particularly under the challenge of the biotroph. Transcript accumulations of the other two subunits Gβ and Gγ were either basal or even lower than the basal level. There was an indication for involvement of JA-mediated pathway in the same situations as activation of LOX1 and COI1 were relatively enhanced in the microbe co-inoculated treatments. Non-increment of SA content as well as transcripts of SA-dependent PR1 suggested non-activation of the SA-mediated signal transduction in the interaction of pea with E. pisi under the stimuli of OKC and T42. Gα1 and 2 transcript accumulations were further correlated with peroxidases activities, H2O2 generation and accumulation in ABA in pea leaves under OKC and T42 stimulations and all these activities were positively correlated with stomata closure at early stage of the biotroph challenge. The microbe-induced physiological responses in pea leaves finally led to reduced E. pisi development particularly in OKC and T42 co-inoculated plants. We conclude that OKC and T42 pretreatment stimulate transcript accumulations of the Gα1 and Gα2 subunits of the heterotrimeric G protein, peroxidases activities and phenol accumulation in pea during infection by E. pisi. The signal transduction was possibly mediated through JA in pea under the stimulus of the microbes and the cumulative effect of the co-inoculated microbes had a suppressive effect on E. pisi conidial development on pea leaves.
Influence of Air Pollution and Climate on Daily Health of Gabonese Students in the Capital (Libreville): A Pilot Study

Air pollution is a global issue affecting billions of people, especially urban populations in low- and middle-income countries. Since air pollution is a health problem that also involves the climate, this study assessed the relationship between the individual health of 50 college students living in Libreville (Gabon) and air quality, temperature, and humidity using low-cost equipment. The study utilised 81 days of data from the air pollution monitoring network in Libreville. These data were paired with measurements of heart rate, breathing, and stress measured using 5 Garmin vívosmart® smartwatches. In addition to the environmental and health data, participants were also asked about their state of health and their lifestyle during the study. We found average concentrations of PM2.5 (25.25 µg/m3) and PM10 (29.50 µg/m3) that exceed the 24-h WHO air quality standards. The daily average of PM1 was around 17.84 µg/m3. Temperatures observed during the study period varied between 27 and 35 °C (mean = 30.15 °C), and humidity was around 51-77% (mean = 59.5%). Overall, the relationships between the environmental conditions and the health observations were negligible, with correlation coefficients R ≤ 0.36. Despite their weakness, coefficients between 0.31 and 0.36 showed that stress levels are associated with temperature, PM2.5 and PM10. The average stress level was associated with PM10 (R = 0.34) and PM2.5 (R = 0.36). Finally, the study reveals that smokers, mosquito repellent users, and fan users have reduced breathing capacities compared to non-smokers, non-users of mosquito repellent products, non-users of fans, users and non-users of air conditioning. The study recommends the use of portable sensors to measure individual exposure to environmental parameters for similar studies, which will resolve the problem of spatial representativeness highlighted in this study. It is also recommended that Gabon's health policies incorporate early warnings of forecast high temperatures or pollution peaks, in order to limit health risks
Comparing two methods of follow up in a multicentre randomised trial

AIMS To evaluate a parental questionnaire as a means of providing outcome measures for a multicentre randomised controlled trial of treatment for post-haemorrhagic ventricular dilatation. METHODS The parents of 88 survivors were sent a questionnaire before a paediatric assessment at the age of 30 months. The parents’ responses to individual questions taken mainly from the Griffiths’ mental development scales and their perception of the child’s ability to see and hear were compared with the paediatric findings. A model, based on the parents’ responses to particular questions, allowed the categorisation of the children as normal, impaired, moderately or severely disabled; this was compared with similar categorisation based on the full paediatric assessment. RESULTS Agreement on items concerning gross motor function ranged between 81 and 99%, concerning dressing between 77 and 80%, concerning feeding between 91 and 99%, and concerning language between 85 and 93%. Similar proportions of children were identified as disabled by the parents (60%) and by the paediatrician (66%). Of 29 children who had developmental quotients less than 70, parents identified 28 as disabled, 18 of them as severely disabled. They were not so good at identifying children with impairments without functional loss. CONCLUSIONS Further work is required but there is sufficient encouragement from the results to pursue this methodology further for use in comparing groups in randomised trials.
Flattening hierarchical scheduling

Recently, the application of virtual-machine technology to integrate real-time systems into a single host has received significant attention and caused controversy. Drawing two examples from mixed-criticality systems, we demonstrate that current virtualization technology, which handles guest scheduling as a black box, is incompatible with this modern scheduling discipline. However, there is a simple solution by exporting sufficient information for the host scheduler to overcome this problem. We describe the problem, the modification required on the guest and show on the example of two practical real-time operating systems how flattening the hierarchical scheduling problem resolves the issue. We conclude by showing the limitations of our technique at the current state of our research.
Kinin Receptor Agonism Restores Hindlimb Postischemic Neovascularization Capacity in Diabetic Mice

Limb ischemia is a major complication of thromboembolic diseases. Diabetes worsens prognosis by impairing neovascularization. Genetic or pharmacological inactivation of the kallikrein-kinin system aggravates limb ischemia in nondiabetic animals, whereas angiotensin I–converting enzyme/kininase II inhibition improves outcome. The role of kinins in limb ischemia in the setting of diabetes is not documented. We assessed whether selective activation of kinin receptors by pharmacological agonists can influence neovascularization in diabetic mice with limb ischemia and have a therapeutic effect. Selective pseudopeptide kinin B1 or B2 receptor agonists resistant to peptidase action were administered by osmotic minipumps at a nonhypotensive dosage for 14 days after unilateral femoral artery ligation in mice previously rendered diabetic by streptozotocin. Comparison was made with ligatured, nonagonist-treated nondiabetic and diabetic mice. Diabetes reduced neovascularization, assessed by microangiography and histologic capillary density analysis, by roughly 40%. B1 receptor agonist or B2 receptor agonist similarly restored neovascularization in diabetic mice. Neovascularization in agonist-treated diabetic mice was indistinguishable from nondiabetic mice. Both treatments restored blood flow in the ischemic hindfoot, measured by laser-Doppler perfusion imaging. Macrophage infiltration increased 3-fold in the ischemic gastrocnemius muscle during B1 receptor agonist or B2 receptor agonist treatment, and vascular endothelial growth factor (VEGF) level increased 2-fold. Both treatments increased, by 50–100%, circulating CD45/CD11b-positive monocytes and CD34+/VEGFR2+ progenitor cells. Thus, selective pharmacological activation of B1 or B2 kinin receptor overcomes the effect of diabetes on postischemic neovascularization and restores tissue perfusion through monocyte/macrophage mobilization. Kinin receptors are potential therapeutic targets in limb ischemia in diabetes.
Pressure mediates angiotensin II-induced arterial hypertrophy and PDGF-A expression.

Angiotensin II (Ang II) may induce arterial hypertrophy either directly or through an increase in arterial pressure. To separate these 2 mechanisms, rats were implanted with osmopumps delivering either Ang II (100 ng x kg-1 x min-1) or saline. 5-Bromo-2'-deoxyuridine (BrdU) was delivered to both groups by osmopump (2.5 microg x kg-1 x min-1). Half of the rats in each group were given minoxidil (9 mg x kg-1 . d-1) in their drinking water. After 14 days, systolic blood pressure was 117+/-2, 124+/-3, and 115+/-2 mm Hg in the control, Ang II-minoxidil, and minoxidil groups, respectively, and 181+/-6 mm Hg in the Ang II group (P<0.05). After perfusion-fixation, the thoracic aorta, carotid artery, small mesenteric artery, external spermatic artery, and kidneys were harvested, paraffin-embedded, and used for morphological measurements, immunohistochemistry for BrdU, and in situ hybridization with a 35S-labeled riboprobe for platelet-derived growth factor-A chain (PDGF-A) mRNA. The walls of the aorta and carotid arteries hypertrophied in the Ang II group only. There were no significant morphological differences in the small arteries. BrdU was negative in all arteries but positive in the renal tubules. Expression of PDGF-A was elevated 8-fold in the thoracic aorta of the Ang II group (P<0.05). These results show that (1) arterial hypertrophy from Ang II infusion occurs in response to elevated arterial pressure, (2) hypertrophy was not associated with hyperplasia or polyploidy of vascular smooth muscle cells, and (3) PDGF-A expression correlated with elevated pressure and arterial wall hypertrophy.
On the role of spatial phase and phase correlation in vision, illusion, and cognition

Numerous findings indicate that spatial phase bears an important cognitive information. Distortion of phase affects topology of edge structures and makes images unrecognizable. In turn, appropriately phase-structured patterns give rise to various illusions of virtual image content and apparent motion. Despite a large body of phenomenological evidence not much is known yet about the role of phase information in neural mechanisms of visual perception and cognition. Here, we are concerned with analysis of the role of spatial phase in computational and biological vision, emergence of visual illusions and pattern recognition. We hypothesize that fundamental importance of phase information for invariant retrieval of structural image features and motion detection promoted development of phase-based mechanisms of neural image processing in course of evolution of biological vision. Using an extension of Fourier phase correlation technique, we show that the core functions of visual system such as motion detection and pattern recognition can be facilitated by the same basic mechanism. Our analysis suggests that emergence of visual illusions can be attributed to presence of coherently phase-shifted repetitive patterns as well as the effects of acuity compensation by saccadic eye movements. We speculate that biological vision relies on perceptual mechanisms effectively similar to phase correlation, and predict neural features of visual pattern (dis)similarity that can be used for experimental validation of our hypothesis of “cognition by phase correlation. ”
Alcohol’s Effect on Host Defense

Alcohol affects many organs, including the immune system, with even moderate amounts of alcohol influencing immune responses. Although alcohol can alter the actions of all cell populations involved in the innate and adaptive immune responses, the effect in many cases is a subclinical immunosuppression that becomes clinically relevant only after a secondary insult (e.g., bacterial or viral infection or other tissue damage). Alcohol’s specific effects on the innate immune system depend on the pattern of alcohol exposure, with acute alcohol inhibiting and chronic alcohol accelerating inflammatory responses. The proinflammatory effects of chronic alcohol play a major role in the pathogenesis of alcoholic liver disease and pancreatitis, but also affect numerous other organs and tissues. In addition to promoting proinflammatory immune responses, alcohol also impairs anti-inflammatory cytokines. Chronic alcohol exposure also interferes with the normal functioning of all aspects of the adaptive immune response, including both cell-mediated and humoral responses. All of these effects enhance the susceptibility of chronic alcoholics to viral and bacterial infections and to sterile inflammation.
A Variable Metric Forward-Backward Method with Extrapolation

Forward-backward methods are a very useful tool for the minimization of a functional given by the sum of a differentiable term and a nondifferentiable one, and their investigation has comprised several efforts from many researchers in the last decade. In this paper we focus on the convex case and, inspired by recent approaches for accelerating first-order iterative schemes, we develop a scaled inertial forward-backward algorithm which is based on a metric changing at each iteration and on a suitable extrapolation step. Unlike standard forward-backward methods with extrapolation, our scheme is able to handle functions whose domain is not the entire space. Both an ${\mathcal O}(1/k^2)$ convergence rate estimate on the objective function values and the convergence of the sequence of the iterates are proved. Numerical experiments on several test problems arising from image processing, compressed sensing, and statistical inference show the effectiveness of the proposed method in comparison to well-performing s.