Miracle-dz/UniFAR-FTUs huggingface dataset:
The Arabidopsis bZIP19 and bZIP23 transcription factors act as zinc-sensors to control plant zinc status

Zinc (Zn) is an essential micronutrient for plants and animals because of its structural and catalytic roles in many proteins. Zn deficiency affects ca. two billion people, mainly those living on plant-based diets that rely on crops from Zn deficient soils. Plants maintain adequate Zn levels through tightly regulated Zn homeostasis mechanisms, involving Zn uptake, distribution and storage, but it was not known how they sense Zn status. We use in vitro and in planta approaches to show that the Arabidopsis thaliana F-group bZIP transcription factors bZIP19 and bZIP23, which are the central regulators of the Zn deficiency response, act as Zn sensors by binding Zn2+ ions to a Zn sensor motif (ZSM). Deletions or modifications of this ZSM disrupts Zn binding, leading to a constitutive transcriptional Zn deficiency response, which causes a significant increase in plant and seed Zn accumulation. Since the ZSM is highly conserved in F-bZIPs across land plants, the identification of the first plant Zn-sensor will promote new strategies to improve the Zn nutritional quality of plant-derived food and feed, and contribute to tackle the global Zn deficiency health problem.
Analytical Evaluation of ABL90 Flex Plus Blood Gas Analyzer for Urea and Creatinine

Background Acute kidney injury is a common complication among hospitalized patients. The availability of creatinine and urea measurements as point-of-care testing provides an alternative strategy to monitor renal function and develop prevention strategies, especially in the emergency services, where reducing waiting times and rapid clinical decisions may be required. Objective The aim of this study was to evaluate if creatinine and urea measurements are interchangeable between ABL90 Flex Plus and three common central laboratory methods. Methods With a multicenter design, creatinine and urea were first analyzed by ABL90 Flex Plus and then by laboratory method: Dimension Vista 1500, Cobas c702, and Architect c16000 according to Clinical and Laboratory Standards Institute EP09-A3 protocol. All measurements were performed in duplicate. Results were evaluated using Passing-Bablok regression and Bland-Altman comparison. Interchangeability of patient results was verified at different clinical decision levels. Results Passing-Bablok regression between the 3 central laboratory methods and ABL90 Flex Plus showed correlation coefficients over 0.998 for creatinine and 0.994 for urea, and despite the presence of proportional and/or constant bias observed in the study, estimated difference was lower than the allowable difference (±15.6% for urea and ±8.9% for creatinine) at clinical decision levels in all cases. Conclusion Creatinine and urea measurements are interchangeable using ABL90 Flex Plus blood gas analyzer compared with 3 central laboratory methods, ensuring no impact on patient care using indistinctly any analyzer.
Stabilizing selection of seasonal influenza receptor binding in populations with partial immunity

Mutations that alter cellular receptor binding of influenza hemagglutinin (HA) have profound effects on immune escape. Despite its high mutation rate, it is not fully understood why human influenza HA displays limited antigenic diversity across circulating viruses. We applied phylogenetic analysis and phylodynamic modeling to understand the evolutionary and epidemiological effects of binding avidity adaptation in humans using net charge as a marker for receptor binding avidity. Using 686 human influenza A/H3N2 HA sequences, we found that HA net charge followed an age-specific pattern. Phylogenetic analysis suggested that many binding variants have reduced fitness. Next, we developed an individual-based disease dynamic model embedded with within-host receptor binding adaptation and immune escape in a population with varied partial immunity. The model showed that mean binding avidity was unable to adapt to values that maximized transmissibility due to competing selective forces between within- and between-host levels. Overall, we demonstrated stabilizing selection of virus binding in a population with increasing partial immunity. These findings have potential implications in understanding the evolutionary mechanisms that determine the intensity of seasonal influenza epidemics.
Phylogeographic structure and mitochondrial DNA variation in true lemmings (Lemmus) from the Eurasian Arctic

Abstract The geographic pattern of mtDNA variation in lemmings from 13 localities throughout the Eurasian Arctic was studied by using eight restriction enzymes and sequencing of the cytochromebregion. These data are used to reveal the vicariant history ofLemmus, and to examine the effect of the last glaciation on mtDNA variation by comparing diversity in formerly glaciated areas to the diversity in non-glaciated areas. Phylogenetic congruence across different Arctic taxa and association between observed discontinuities, and probable Pleistocene barriers, suggest that glacial-interglacial periods were crucial in the vicariant history ofLemmus. Differences in amount of divergence (2.1–9.1%) across different historical barriers indicate chronologically separate vicariant events during the Quaternary. Populations from a formerly glaciated area are no less variable than those in the non-glaciated area. Regardless of glaciation history, no population structure and high haplotype diversity were found within geographic regions. The lack of population structure indicates that populations with high ancestral haplotype diversity shifted their distribution during the Holocene, and that lemmings tracked a changing environment during the Quaternary without reduction of effective population size.
Chromosome-scale inference of hybrid speciation and admixture with convolutional neural networks

Inferring the frequency and mode of hybridization among closely related organisms is an important step for understanding the process of speciation and can help to uncover reticulated patterns of phylogeny more generally. Phylogenomic methods to test for the presence of hybridization come in many varieties and typically operate by leveraging expected patterns of genealogical discordance in the absence of hybridization. An important assumption made by these tests is that the data (genes or SNPs) are independent given the species tree. However, when the data are closely linked, it is especially important to consider their non-independence. Recently, deep learning techniques such as convolutional neural networks (CNNs) have been used to perform population genetic inferences with linked SNPs coded as binary images. Here we use CNNs for selecting among candidate hybridization scenarios using the tree topology (((P1, P2), P3), Out) and a matrix of pairwise nucleotide divergence (dXY) calculated in windows across the genome. Using coalescent simulations to train and independently test a neural network showed that our method, HyDe-CNN, was able to accurately perform model selection for hybridization scenarios across a wide-breath of parameter space. We then used HyDe-CNN to test models of admixture in Heliconius butterflies, as well as comparing it to a random forest classifier trained on introgression-based statistics. Given the flexibility of our approach, the dropping cost of long-read sequencing, and the continued improvement of CNN architectures, we anticipate that inferences of hybridization using deep learning methods like ours will help researchers to better understand patterns of admixture in their study organisms.
Grazing damage in the old forest lichen Lobaria pulmonaria increases with gastropod abundance in deciduous forests

Abstract Gastropod abundance was quantified in forest litter around 33 trees harbouring Lobaria pulmonaria in southern Norway. In total, 1709 snails representing 28 species were found, and the number of snail species strongly increased with the total number of specimens found. Number of snail species, as well as snail abundance, was highest around trees on high pH soils. There was a positive relationship between number of snail specimens and cover of grazing traces on L. pulmonaria, presumably because calcareous soils facilitate both litter dwelling and climbing gastropods. The results suggest that gastropods may limit the distribution of L. pulmonaria in calcareous broad-leaved forests.
Vascular plant compositional gradients within and between Iowa fens

Abstract Question: What is the nature and relative importance of compositional gradients within- and between fens? Location: Iowa, USA. Methods: 506 0.5 m × 0.5 m quadrats were sampled from 31 fens across a 550 km extent. Presence/absence of all vascular plant taxa, plus the non-vascular genera Sphagnum and Chara, and values for 24 environmental variables were noted. Global Non-Metric Multidimensional Scaling and Monte Carlo tests were used to describe compositional variation and identify significant environmental co-variables. Model-based cluster analysis was used to identify the optimal number of groups supported by the data, while k-means clustering was used to assign each quadrat to a group. The number of occurrences (and frequency) of each species within each group was calculated. Two-dimensional 95% Gaussian confidence intervals, ANOVA, correlation coefficient homogeneity tests, log-linear modelling, and Fisher's exact tests were used to document patterns of compositional change. Results: Two stable axes of variation were identified: the first being most closely correlated with soil pH, Mg, Ca, P, S, vegetation height, surface and −10 cm soil temperature, site area, perimeter, perimeter/area ratio, growing season, and air temperature, with the second being most correlated to soil moisture, N, disturbance level, % organic matter, hummock height, N-S coordinate, and precipitation. Individual sites harboured between 20–47% of total compositional variation, with 28% of Axis 1 and 55% of Axis 2 scores being contained within-sites. Five compositional regions were identified that differed in the proportion of calciphile and hydrophile species. Compositional groups differed significantly between geologic types. Conclusions: While the principal axis of variation (corresponding to the rich-poor fen gradient) is present largely between sites, the second axis (corresponding to water level) is largely repeated within sites. Documentation and protection of vegetation patterns and species diversity within Iowa fens will thus require consideration of multiple sites across the landscape. Nomenclature: Nekola (1994).
A Role for Nickel in Cyanobacterial Nitrogen Fixation and Growth via Cyanophycin Metabolism

Summary: When nickel-depleted cells of Anabaena cylindrica with nitrogenase repressed by growth on ammonia or into late stationary phase) were used to re-initiate nitrogen-fixing growth in fresh nickel-depleted medium a pronounced growth lag was observed. The growth lag was not observed in the presence of NiSO4 (0.68 μM). It was associated with delayed heterocyst differentiation, delayed nitrogenase synthesis and inhibition of pigment synthesis. During the lag a pronounced but transient accumulation of cyanophycin was observed, followed by an accumulation of urea in the growth medium. It is proposed that nickel depletion results in a diversion of ammonia from protein synthesis into cyanophycin, thereby delaying the de novo synthesis of proteins and enzymes required for the synthesis of active nitrogenase.
Reproduction is costly in an infected aquatic insect

Internal energy reserves of animals are limited, and the current investment in reproduction often decreases survival or future reproductive success. Some studies showed that copulatory activities impair the strength of immune function in insects, while the recent evidence is contradictory. In this study we tested whether copulatory activity affects the rate of encapsulation response in males of Calopteryx splendens damselfly in allopatric populations, and in sympatric populations where C. splendens stay together with their superior competitor C. virgo. We also counted the number of eugregarines, which are common parasites of damselflies. Copulation activity did not affect the immunity of C. splendens males in allopatric populations. In sympatric populations C. splendens males had more gut parasites, and we found a significant interaction between parasite number and copulatory activity on the rate of encapsulation. Our results suggest that the costs of reproduction are higher in infected males, which may affect reproductive investment and sexual selection.
Exposure to interferon‐γ during synaptogenesis increases inhibitory activity after a latent period in cultured rat hippocampal neurons

Certain disorders of the nervous system may have their origin in disturbances in the development of synaptic connections and network structure that may not become overt until later in life. As inflammatory cytokines can influence synaptic activity in neuronal cultures, we analysed whether cytokine exposure during synaptogenesis can lead to imbalances in a neuronal network. Short‐term application of interferon‐γ (IFN‐γ), but not tumour necrosis factor‐α, during peak synaptogenesis (but not before or after) in Sprague–Dawley rat hippocampal cultures, caused both a decrease in the frequency of spontaneous excitatory postsynaptic currents (EPSCs) and an increase in the frequency of spontaneous inhibitory postsynaptic currents (IPSCs). These effects were only detected in recordings made weeks later. This was not due to a depression of glutamatergic synapses or to a change in the relative number of neurons containing glutamic acid decarboxylase (GAD). There was an increase in the average amplitude of miniature IPSCs, and in GAD‐expressing neurons the amplitude of miniature EPSCs were larger as well as the responses to glutamate. This indicates that IFN‐γ‐treatment induced increased inhibition via postsynaptic changes. These effects of IFN‐γ treatment were not observed when neuronal nitric oxide synthase was inhibited. Our study therefore shows that exposure to IFN‐γ during a restricted period of development, which coincides with the peak of excitatory synaptogenesis, can cause progressive changes in synaptic activity in the network. Thus, cytokine exposure at a critical period of development may constitute a ‘hit‐and‐run’ mechanism for certain nervous system disorders that become manifest after a latency period.
Female and Male Mediation of Incompatibility Modifications during the Tristyly-Distyly Transition in Oxalis alpina

Transitions between breeding systems offer an opportunity to understand the selective forces underlying these changes. In the evolutionary transition from tristyly to distyly, changes in tristylous self-incompatibility (SI) may be associated with modifications of female function, male function, or both. To test the hypothesis that modifications of pollen incompatibility reactions are associated with these changes, we used reciprocal factorial crosses in two Oxalis alpina populations that differed in their incompatibility relationships. Contrary to predictions, the population exhibiting stronger tristylous SI showed significant variation in both female and male components of incompatibility. The population with more highly modified tristylous SI at a putatively later stage in the evolution of distyly had less variation in both paternal and maternal control of incompatibility. The more highly modified population also showed evidence of correlations between the changes in maternal and paternal components of tristylous SI and between incompatibility and changes in floral morphology. Comparisons of these populations indicate that modifications of both female and male components of tristylous SI may occur before changes in floral morphology during the transition from tristyly to distyly in O. alpina.
Erythromycin inhibits neutrophilic inflammation and mucosal disease by upregulating DEL-1.

Macrolide antibiotics exert anti-inflammatory effects; however, little is known regarding their immunomodulatory mechanisms. In this study, using two distinct mouse models of mucosal inflammatory disease (LPS-induced acute lung injury and ligature-induced periodontitis), we demonstrated that the anti-inflammatory action of erythromycin (ERM) is mediated through upregulation of the secreted homeostatic protein DEL-1. Consistent with the anti-neutrophil recruitment action of endothelial cell-derived DEL-1, ERM inhibited neutrophil infiltration in the lungs and the periodontium in a DEL-1-dependent manner. Whereas ERM (but not other antibiotics such as josamycin and penicillin) protected against lethal pulmonary inflammation and inflammatory periodontal bone loss, these protective effects of ERM were abolished in Del1-deficient mice. By interacting with the growth hormone secretagogue receptor (GHSR) and activating JAK2 in human lung microvascular endothelial cells, ERM induced C/EBPβ-dependent DEL-1 transcription, which was mediated by MAPK p38. Moreover, ERM reversed IL-17-induced inhibition of DEL-1 transcription, in a manner that was not only dependent on JAK2 but also on PI3K/AKT signaling. As DEL-1 levels are severely reduced in inflammatory conditions and with aging, the ability of ERM to upregulate DEL-1 may be a novel approach for the treatment of inflammatory and aging-related diseases.
Texture and Differential Stress Development in W/Ni-Co Composite after Rotary Swaging

Knowledge of texture and residual stresses in tungsten heavy pseudoalloys is substantial for the microstructure optimization. These characteristics were determined in cold and warm rotary swaged W/NiCo composite with help of neutron diffraction. The results were discussed in view of the observed microstructure and mechanical properties. The investigated bars consisted of tungsten agglomerates (bcc lattice) surrounded by NiCo-based matrix (fcc lattice). No preferential crystallographic orientation was found in the as-sintered bar. A strong texture was formed in both the tungsten agglomerates (<101> fiber texture parallel to the swaging axis) and in the NiCo-based matrix (<111> fiber texture) after rotary swaging. Although usually of double-fiber texture, the <001> fiber of the fcc structures was nearly missing in the matrix. Further, the cold-swaged bar exhibited substantially stronger texture for both phases which corresponds to the higher measured ultimate tensile strength. The residual stress differences were employed for characterization of the stress state of the bars. The largest residual stress difference (≈400 MPa) was found at the center of the bar deformed at room temperature. The hoop stresses were non-symmetrical with respect to the swaging axis, which was likely caused by the elliptical cross section of the as-sintered bar.
Modelling the attack success of planktonic predators: patterns and mechanisms of prey size selectivity

A mathematical model of the attack success of planktonic predators (fish larvae and carnivorous copepods) is proposed. Based on a geometric representation of attack events, the model considers how the escape reaction characteristics (speed and direction) of copepod prey affect their probability of being captured. By combining the attack success model with previously published hydrodynamic models of predator and prey perception, we examine how predator foraging behaviour and prey perceptive ability affect the size spectra of encountered and captured copepod prey. We examine food size spectra of (i) a rheotactic cruising predator, (ii) a suspension-feeding hovering copepod and (iii) a larval fish. For rheotactic predators such as carnivorous copepods, a central assumption of the model is that attack is triggered by prey escape reaction, which in turn depends on the deformation rate of the fluid created by the predator. The model demonstrates that within a species of copepod prey, the ability of larger stages to react at a greater distance from the predator results in increased strike distance and, hence, lower capture probability. For hovering copepods, the vorticity field associated with the feeding current also acts in modifying the prey escape direction. The model demonstrates that the reorientation of the prey escape path towards the centre of the feeding current's flow field results in increased attack success of the predator. Finally, the model examines how variability in the kinetics of approach affects the strike distance of larval fish. In cases where observational data are available, model predictions closely fit observations.
Activity Patterns and Parasitism Rates of Fire Ant-Decapitating Flies (Diptera: Phoridae: Pseudacteon spp.) in Their Native Argentina

Abstract This work describes the annual and daily activity patterns of two parasitoid fly communities of the fire ant Solenopsis invicta (Hymenoptera: Formicidae) in their native range in Argentina. Pseudacteon (Diptera: Phoridae) flies were censused monthly for 1 yr at two sites in northwestern Corrientes province. Additionally, parasitism rates of S. invicta colonies naturally attacked in the field by Pseudacteon flies are reported for the first time from its native habitat. In total, 4,528 flies (86.3% females) of eight Pseudacteon species were collected attacking ants in the field. Pseudacteon litoralis Borgmeier and Pseudacteon nocens Borgmeier represented 71–79% of female flies censused in both sites. Most species were active throughout the year, although abundances were variable over time and between sites. The highest occurrence peaks of flies were recorded in spring, whereas the lowest occurrence was in summer. Fly abundance was higher close to dusk, whereas species diversity was highest at midday. Relationships among species were established based on their activity patterns and genetic proximity. The presence and abundance of four species were explained by climatic variables, whereas two species may have inherited similar circadian rhythms from a common ancestor. Overall, the parasitism rate by the nine species recorded was very low (0.24%). The highest percentage of parasitized workers was found in spring (0.5%) and occurred within the most complex habitat (gallery forest). The highest parasitism rate per site and colony was also for this habitat in spring (1.16 and 2.81%, respectively). The highest rates of emergence were recorded for Pseudacteon nudicornis Borgmeier.