Miracle-dz/UniFAR-FTUs huggingface dataset:
Endothelial Pannexin 1 Channels Control Inflammation by Regulating Intracellular Calcium

Key Points TNF-α signals via NF-κB to promote Panx1 expression. Panx1 channel signaling can regulate [Ca2+]i in HUVECs. Increased Panx1 regulates HUVEC IL-1β release and monocyte binding. Visual Abstract The proinflammatory cytokine IL-1β is a significant risk factor in cardiovascular disease that can be targeted to reduce major cardiovascular events. IL-1β expression and release are tightly controlled by changes in intracellular Ca2+ ([Ca2+]i), which has been associated with ATP release and purinergic signaling. Despite this, the mechanisms that regulate these changes have not been identified. The pannexin 1 (Panx1) channels have canonically been implicated in ATP release, especially during inflammation. We examined Panx1 in human umbilical vein endothelial cells following treatment with the proinflammatory cytokine TNF-α. Analysis by whole transcriptome sequencing and immunoblot identified a dramatic increase in Panx1 mRNA and protein expression that is regulated in an NF-κB–dependent manner. Furthermore, genetic inhibition of Panx1 reduced the expression and release of IL-1β. We initially hypothesized that increased Panx1-mediated ATP release acted in a paracrine fashion to control cytokine expression. However, our data demonstrate that IL-1β expression was not altered after direct ATP stimulation in human umbilical vein endothelial cells. Because Panx1 forms a large pore channel, we hypothesized it may permit Ca2+ diffusion into the cell to regulate IL-1β. High-throughput flow cytometric analysis demonstrated that TNF-α treatments lead to elevated [Ca2+]i, corresponding with Panx1 membrane localization. Genetic or pharmacological inhibition of Panx1 reduced TNF-α–associated increases in [Ca2+]i, blocked phosphorylation of the NF-κB–p65 protein, and reduced IL-1β transcription. Taken together, the data in our study provide the first evidence, to our knowledge, that [Ca2+]i regulation via the Panx1 channel induces a feed-forward effect on NF-κB to regulate IL-1β synthesis and release in endothelium during inflammation.
Sex-specific transgenerational plasticity in threespined sticklebacks

Sex-specific selection pressures can generate different phenotypic optima for males and females in response to the current environment, i.e. sex differences in phenotypic plasticity. Less widely appreciated is the possibility that transgenerational plasticity (TGP) can also depend on sex. Sex-specific TGP is potentially of great evolutionary significance, as it is a mechanism by which mothers and fathers can exert different effects on offspring traits and by which potentially adaptive traits can persist selectively across generations via only daughters or sons. Here, we demonstrate that maternally- and paternally-mediated TGP in response to predation risk have largely distinct effects on offspring traits in threespined sticklebacks (Gasterosteus aculeatus). Predator-exposed fathers produced sons that were more risk-prone, while predator-exposed mothers produced more anxious sons and daughters. Further, when combined together, maternal and paternal environments on offspring survival were nonadditive. Such sex-specific effects could occur if predation risk causes mothers and fathers to activate different developmental programs in sons versus daughters. Consistent with this hypothesis, offspring brain gene expression profile depended on whether their mother and/or father had been exposed to risk, and the influence of maternal and paternal environments varied between male and female offspring. Altogether these results draw attention to the potential for sex to influence patterns of TGP, and raise new questions about the evolution of plasticity at the interface between sexual conflict and parent-offspring conflict, with paternal strategies, maternal strategies, and offspring counter adaptations all ultimately dictating offspring phenotypes. Significance TGP helps organisms cope with environmental change by bridging the gap between within-generational plasticity and long-term evolutionary change. Sex-specific TGP may allow mothers and fathers to selectively alter the phenotypes of their sons and daughters in response to the environment with a greater degree of precision than genetic inheritance and in ways that match the distinct life-history strategies of males and females. By isolating cues coming from mothers versus fathers and separately evaluating phenotypic effects in sons versus daughters, we show that interactions between maternal cues, paternal cues, and offspring sex are integral to understanding when and how the past environment influences future phenotypes, and the conditions that favor the evolution of TGP.
Effects of
 Epichloë
 endophyte infection on growth, physiological properties and seed germination of wild barley under saline conditions

Salinity is a worldwide problem in agricultural production and is a major abiotic stress for plants in semi‐arid or arid regions; a third of irrigated land and a fifth of cropland are affected by salinity (Muscolo, Sidari, & Panuccio, 2003; Shrivastava & Kumar, 2015). Wild barley (Hordeum brevisubulatum), a perennial forage species, has strong salinity resistance and good productivity. It is the dom‐ inant species in alkalized meadows in northern China and has been widely cultivated in Jilin, Inner Mongolia, Hebei, Gansu, Qinghai and Xinjiang provinces of China (Jia, 1987). In addition, numerous wild Received: 2 April 2019 | Revised: 17 August 2019 | Accepted: 19 August 2019
The regulation of exercise intensity by ratings of perceived exertion and by the palpation technique of heart rate determination

Twenty-nine college age (18 to 30 years) males were randomly distributed into three groups: Group I (THR), Group II (RPE)and Group III (No Prescription). All subjects underwent a series of at least two maximal and six submaxima1 exercise tests. Only the submaximal tests differed among the three groups. Group I (THR) was pro­ vided with a THR range equivalent to 60% and 70% of their maximal capacity as calculated by Karvonen's (Karvonen et al. 1957) formula. This group was trained to use the palpation technique and instructed to exercise at intensities within their THR range by using this technique. A THR range was also calculated for Group II (RPE), however this group was not told what that range was in terms of heart rate. During the first two submaxima1 sessions. Group II's intensity of exercise was controlled in order to maintain the target level of intensity while the subjects rated their perceived exertion. In the subsequent four submaximal tests. Group II was instructed to maintain the prescribed level of exercise intensity solely by monitoring their RPE. Group III (No Prescription) served as a control group. They were instructed to main­ tain an intensity of exercise similar to that which they would if they were exercising on their own. The data was analyzed to determine the effectiveness of RPE as an alternative to the THR method, and to validate the accuracy of the palpation technique at intensities of 60% to 70% of maximum. The
Confined filaments in soft vesicles - case of sickle red blood cells

A semi-rigid filament confined in a soft vesicle of similar size can mutually deform each other. An important example from biological context is Hemoglobin-S (HbS) fibers which polymerize inside red blood cell (RBC). The fibers deform the healthy RBC into sickle-like shape causing difficulty in blood flow through capillaries. Using an area difference elasticity (ADE) model for RBC and a worm-like chain model for the HbS fibers, confined within RBC, we study the shape deformations at equilibrium. We also consider multiple filaments and find that confinement can generate multipolar RBC shapes and can also promote helical filament conformations. The same model, in different parameter regime, reproduces tubulation for phospholipid vesicles, as seen in experiments, when microtubules are confined in the vesicle. We conclude that with a decrease in the surface area to volume ratio, and membrane rigidity, the vesicle prefers tubulation over sickling. Our simulations can access various non-axisymmetric shapes, which have been observed experimentally, both in the context of sickle RBC and phospholipid vesicles, but have so far remained beyond the scope of variational methods.
Expression and Purification of a Mammalian Protein: Cytosolic Domain of IRE1α from Insect Sf21 Cells

Eukaryotic proteins can be expressed in different heterologous systems. However, mammalian proteins in general have specific post-translational processing requirements that may not be fulfilled by a regular bacterial expression system. In this study, we use an insect cell system to express a mammalian protein of interest. Spodoptera frugiperda (Sf21) cells were used in conjunction with a baculoviral expression system to produce the cytosolic domain (CD) of IRE1, an endoplasmic reticulum (ER) stress sensor protein. Inositol Requiring Enzyme 1 (IRE1) is a dual function kinase and endoribonuclease protein that cleaves X-box binding protein (XBP1) mRNA. We used the pFastBac plasmid to insert the coding sequence into a recombinant bacmid shuttle vector which was then used to infect Sf21 cells. The expressed protein was then purified with an MBPTrap column to obtain >85% pure protein.
Genomics of divergence and hybridisation in the genus Antirrhinum L.

viii General introduction . 10 Speciation . 10 Evolutionary radiations . 11 Hybridisation and hybrid zones . 13 Genomics . 14 Genomic architecture of speciation . 16 The genus Antirrhinum . 18 Aims and approaches . 21 The phylogeny of Antirrhinum reveals multiple transitions in flower colour and morphology . 25 Abstract . 25. 25 Introduction . 26 Methods . 30 Specimen sampling and sequencing . 30 Processing and alignment of RAD-seq data . 31 Phylogenetic analyses . 33 Evaluating genetic structure . 33 Hybridisation analysis . 34 Ancestral state reconstruction of vegetative and reproductive characters . 34
Weed leucaena and its significance, implications and control

Keynote paper presented at the International Leucaena Conference, 1‒3 November 2018, Brisbane, Queensland, Australia.Leucaena (Leucaena leucocephala) is widely recognized in many countries as a commercially valuable plant, particularly when used as a nutritious fodder in subtropical and tropical regions. However, it is also considered an environmental weed in some countries due to its ability to form dense infestations in disturbed areas, where it is not proactively managed or grazed. These different perspectives have made leucaena a contentious species. Ideally, landholders and relevant jurisdictions in charge of invasive species need to work together to minimize its spread as a weed and manage existing infestations. To date, the response has been varied, ranging from no action through to some jurisdictions formally recognizing leucaena as an environmental weed within relevant legislation and applying requirements to minimize its impact. Between these extremes, there are initiatives such as an industry Code of Practice (i.e. The Leucaena Network in Australia), recommending that those growing leucaena adhere to certain principles and practices to minimize the risk of spread from their operations. The biology of weed leucaena (e.g. large seed production, relatively long-lived seed banks) and the situations in which it spreads (e.g. roadsides and riparian systems) pose management challenges to landholders and relevant jurisdictions. Adaptive management and experimental research are necessary to identify effective control strategies for a range of situations.
Coastal songbird condition on migratory stopover varies by geographical location and bird age

ABSTRACT The period of migration can pose significant energetic challenges as birds attempt to reach their destinations. Suitable stopover habitat is, therefore, important to the success of migrating individuals, especially as they move along major migration corridors and geographic features, like coastlines. In this study, we used metrics of individual body condition (i.e. fat score, size-corrected body mass, and refueling rate) of fall migrants as they moved across the Gulf of Maine region, a complex coastal landscape. We investigated the extent to which these body condition indices varied by stopover site geography (island vs. mainland) and how these spatial patterns varied with species-specific characteristics such as migratory distance, foraging guild, and age. Geography was an important factor explaining variation in all 3 condition indices, and age explained additional variance in 2 of the 3. In general, individuals captured on islands exhibited significantly lower energetic condition than individuals on the mainland, and this pattern held true across all migratory strategies and foraging guilds. Immature individuals had, on average, lower energy reserves, with less fat and lower size-corrected mass than adults among all stopover sites. We also found that at all sites, size-corrected body mass, on average, significantly increased over the capture day, providing evidence that both island and mainland sites provided energetically beneficial stopover habitat. Our finding that birds offshore are in lower body condition at capture than those along the coast is suggestive that birds use mainland sites for longer stopover bouts than island sites, or that poorer condition birds reorient to land during over-water movements disproportionately use off-shore islands as their initial landing area. Decreases in either island or mainland stopover site availability or quality may affect individual fitness, with population-level consequences, but through different ways.
Performance of energy and protein metabolism of female water buffaloes during early postpartum period

An amount of 30 crossbred female buffaloes was used to evaluate blood levels of glucose, cholesterol, triglycerides, total proteins and urea during the first eight weeks postpartum. Blood samples were obtained from the jugular vein once a week. Biochemical analyzes were performed through the enzymatic calorimetric method and readings were carried out by absorption spectrophotometry. A mixed generalized linear model was used. Postpartum weeks showed a significant effect on the performance of serum indicators (P <.0001). Different was observed for the number of parturitions and milk production during the first 60 days. There was an increase (P <.0001) of glycemia (2.67 - 3.62 mmol/L) and uremia (6.15 - 6.81 mmol/L) from the first to the fifth and sixth week, respectively, although a gradual decrease was observed in the subsequent weeks. Cholesterol (1.04 - 1.80 mmol/L) and triglycerides (0.26 - 0.80 mmol/L) concentrations showed continuous increase during the study (P <.0001). Total proteins showed decrease (P <.0001) in their concentrations from the first to the fifth week (82.48 - 76.76 g/L), while a progressive increase was observed in the following weeks. It was demonstrated that, during the first eight postpartum weeks, there are variations in the concentrations of energy and protein metabolism indicators in buffaloes, mainly due to the increase of milk production and mobilization of their body reserves, as a consequence of metabolic imbalance between nutrient income and energy required. Keywords: female buffaloes, blood indicators, lactation, postpartum
Influences of blackberry margins on population dynamics of Drosophila suzukii and grape infestation in adjacent vineyards

Understanding the dynamics of pest insect populations in relation to the presence of non‐crop habitats and infestation levels of adjacent crops is essential to develop sustainable pest management strategies. The invasive pest species Drosophila suzukii (Diptera: Drosophilidae) is able to utilize a broad range of host plants. In viticulture, scientific risk assessment for D. suzukii has only recently started and studies assessing the effects of field margins containing wild host plants on D. suzukii population dynamics and on infestation risks in adjacent vineyards are lacking. Thus, in a one‐year field study, the role of different field margins on fly abundance and crop infestation in adjacent vineyards of Vitis vinifera, variety “Pinot Noir,” were investigated. Different monitoring methods were conducted to assess fly distribution, sex ratio and grape infestation in 14 vineyards adjacent to field margins containing either blackberry (BB) Rubus spp. or non‐host (NH) plants. Our results show that blackberries strongly enhanced D. suzukii abundance within field margin vegetation all year long, whereas fly abundance in vineyards adjacent to BB margins was just enhanced in some seasonal periods. Moreover, the influence of BB margins was limited by distance. However, high fly numbers in BB field margins did result in zero egg infestation of “Pinot Noir” berries. These results may have important implications for winegrowers to make efficient management decisions: regardless of high abundance of adult D. suzukii, only grape berry monitoring can assess the actual infestation risk and the potential need to take management action.
Homeostatic plasticity rules that compensate for cell size are susceptible to channel deletion

Neurons can increase in size dramatically during growth. In many species neurons must preserve their intrinsic dynamics and physiological function across several length scales. For example, neurons in crustacean central pattern generators generate similar activity patterns despite multiple-fold increases in their size and changes in morphology. This scale invariance hints at regulation mechanisms that compensate for size changes by somehow altering membrane currents. Using conductance-based neuron models, we asked whether simple activity-dependent feedback can maintain intrinsic voltage dynamics in a neuron as its size is varied. Despite relying only on a single sensor that measures time-averaged intracellular calcium as a proxy for activity, we found that this regulation mechanism could regulate conductance densities of ion channels, and was robust to changes in the size of the neuron. By mapping changes in cell size onto perturbations in the space of conductance densities of all channels, we show how robustness to size change coexists with sensitivity to perturbations that alter the ratios of maximum conductances of different ion channel types. Our findings suggest that biological regulation that is optimized for coping with expected perturbations such as size changes will be vulnerable to other kinds of perturbations such as channel deletions.
A Study on a Correlation between a Predictive Model of Motion Pictures Imitating the Predictive Coding of the Cerebral Cortex and Brain Activity

In recent years, deep neural networks inspired by the notion of predictive coding have been shown to make accurate predictions of future frames. In this study, we focus on a predictive neural network, one of such implementations to evaluate the relationship between natural and artificial neural networks. By using PredNet, a predictive neural architecture, we show that representations extracted from the architecture are correlative with brain activities evoked by natural movie stimuli. Our result gives a verification result on the theoretical hypothesis of predictive coding.
Assessing the potential of environmental DNA metabarcoding for monitoring Neotropical mammals: a case study in the Amazon and Atlantic Forest, Brazil

The application of environmental DNA (eDNA) metabarcoding as a biomonitoring tool has greatly increased in the last decade. However, most studies have focused on aquatic macro-organisms in temperate areas (e.g., fishes). We apply eDNA metabarcoding to detect the mammalian community in two high-biodiversity regions of Brazil, the Amazon and Atlantic Forest. We identified critically endangered and endangered mammalian species in the Atlantic Forest and Amazon respectively and found congruence with species identified via camera trapping in the Atlantic Forest. In light of our results, we highlight the potential and challenges of eDNA monitoring for mammals in these high biodiverse areas.
Mycophenolate mofetil plus prednisolone combination therapy for necrotising leukoencephalitis in a dog: long-term clinical observation, serial imaging analysis and histopathological findings

An 8-year-old intact male mixed-breed dog presented with tetraparesis, right side head tilt, and cluster seizure-like episodes. Based on the magnetic resonance imaging and cerebrospinal fluid analysis results, meningoencephalitis of an unknown aetiology was strongly suspected. The patient survived for 963 days under mycophenolate mofetil plus prednisolone therapy and was ultimately diagnosed with necrotising leukoencephalitis. This report describes the clinical findings, the serial magnetic resonance imaging characteristics, and the histopathologic features of a case of necrotising leukoencephalitis and the long-term survival after mycophenolate mofetil plus prednisolone therapy.
The complete mitochondrial genomes of two endangered bitterling Acheilognathus tabira tohokuensis and A. tabira erythropterus (Cyprinidae, Acheilognathinae)

Abstract Acheilognathus tabira (tabira bitterling) comprises of 5 subspecies, all of which are endangered. In this study, the mitochondrial genome (mitogenome) of the 2 subspecies, A. tabira tohokuensis and A. tabira erythropterus, whose mitogenomes have not been reported previously, was determined. The total lengths of A. tabira tohokuensis and A. tabira erythropterus mitogenomes were 16,774 bp and 16,770 bp, respectively, and were noted as slightly AT-rich. Phylogenetic analysis revealed that these 2 subspecies of A. tabira were the most closely related, out of the 5 subspecies. The deciphered mitogenomes would be useful for conservation and evolutionary studies.
Population-level sensitivity to landscape variables reflects individual-based habitat selection in a woodland bat species

Understanding the relationship between habitat quality and population dynamics is fundamental for long-term management and range predictions in ecology. However, habitat suitability is generally only investigated at the individual scale, as it is the case for the lesser horseshoe bat (Rhinolophus hipposideros), a species of conservation concern. Using a statistical modelling approach and census data of 94 lesser horseshoe bat colonies located in Brittany (France), we analysed the effect of landscape composition and configuration on the demography of surveyed maternity colonies (i.e. colony size, fecundity and growth rate), and compared our result to those provided by individual-based studies. Our results validated that the landscape in a 500-meter buffer around colonies (core foraging area) is crucial for population size and dynamics, and confirmed the positive influence of broadleaved woodland proportion on bat colony size. We revealed a positive effect of lakeshores and riverbanks on colony size and growth rate, underlying the importance of these habitats for the long-term conservation of this non-migratory forest species. Importantly, our results refine previous knowledge concerning the threat posed by the intensification of human activities (e.g. urbanization, agriculture, habitat fragmentation), and highlight the negative effect of large and regular patches of artificial and crop lands and of open land patches shape complexity on all demographic variables investigated. Finally, by confirming and specifying the conclusions of previous individual level studies about lesser horseshoe bats’ habitat selection and quality requirements, our results support the dependence of population dynamics and associated conservation management to individual behaviour and sensitivity.