Miracle-dz/UniFAR-FTUs huggingface dataset:
Activating NK- receptors, homing selectins and inhibitory Siglecs recognize EBOLA-GP and HPV-L1NK

The Ebola virus glycoprotein (EBOV)-GP is extensively glycosylated. Its expression induces a physical alteration of surface adhesion molecules, which causes cell rounding and detachment of the infected cells. This phenomenon likely plays a crucial role in viral pathogenicity. In this study, we show that such morphological changes are cell line-dependent as well as dependent on the surface proteins that interact with EBOV-GP in cis and trans. We have generated data showing that natural killer (NK) cell receptors (NCRs: NKp44 and NKp46), selectins (CD62E/P/L) and inhibitory Siglecs function as receptors for Ebola-GP and human papilloma virus (HPV-L1). We used HEK293 cells transfected with Ebola-GP and recombinant fusion proteins containing the extracellular domain of each of these receptors linked to the Fc of human IgG1, which showed significant differences in their virus-binding behavior compared to HEK293 cells transfected with empty vector. Further, to demonstrate that EBOV-GP is a ligand for NKp44 and other NK-receptors, and to investigate their role in immune escape, we also used human HEK-293, HeLa- and hamster CHO-GP-transfectants. Our data show that the NK receptors NKp44 and NKp46 play a key role in recognizing EBOV (Ebolavirus) and strongly suggest that other inhibitory (Siglec-7, Siglec-5) and non-inhibitory homing receptors (P-Selectin, L-Selectin, E-Selectin, and DC-SIGNR/DC-SIGN) take part in the interaction with virus particles. In addition, we show that NKp44, and NKp46, Siglec-7, and -5, and P-, L-, E-selectins as well as of and DC-SIGNR/DC-SIGN bind to the artificial viral envelope of a lentiviral vector that contains EBOV-GP. Altogether we prove that NCRs and a range of other inhibitory and activating receptors can interact with viral envelope/capsid proteins and that such interaction could play an important role in the elimination of virus infected cells. Our findings could be used to develop new strategies for prevention and treatment of infections by these viruses. Author summary The innate immune system is able to recognize specifically certain virus components. Here we show that activating NK-cell receptors (NKp44, and NKp46) are involved in such interaction by using HEK293 and CHOK1 cells transfected with the Ebola virus glycoprotein (EBOV-GP) and by binding studies with purified EBOV-GP. In detail, we have found moderate to strong affinity of Siglecs (Siglec-7, and -5), selectins (P-, L-, E-Selectin) and DC-SIGNR/DC-SIGN to purified EBOV-GP, and to cells transfected with EBOV-GP as well as to the envelope of a lentiviral vector carrying the EBOV-GP. Our findings show that NKp44, and NKp46, Siglec-7, and -5, as well as P-and L-selectins have a strong affinity to EBOV-G.
Patterns of seed rain and seedling regeneration in abandoned agricultural clearings in a seasonally dry tropical forest in India

Abstract: Forest recovery in abandoned pastures and agricultural fields is often impeded, therefore it is important to understand the factors limiting regeneration. Patterns of seed arrival and regeneration in five abandoned agricultural clearings nested within a seasonally dry tropical forest in India were examined along five transects radiating from the forest edge into the clearings. Wind-dispersed seeds dominated the seed arrival in clearings compared with vertebrate-dispersed seeds: 5563 wind-dispersed seeds and 1094 vertebrate-dispersed seeds of 14 and 13 tree species, respectively, were recorded. Numbers of the former declined steeply with increasing distance from the forest, whereas the latter showed no evident pattern with distance. Seeds of the invasive herb, Chromolaena odorata, were abundant in clearings. Although wind-dispersed seeds greatly outnumbered vertebrate-dispersed seeds, seedlings and saplings of vertebrate-dispersed species were three times more abundant than those of wind-dispersed species, indicating distinct differences in patterns of actual and effective seed dispersal. This points to recruitment limitation, and suggests that seed arrival may not be the principal barrier to regeneration in these clearings. Nonetheless, the clearings are likely to revert to forest over time.
Recent increases in assemblage rarity are linked to increasing local immigration

As pressures on biodiversity increase, a better understanding of how assemblages are responding is needed. Because rare species, defined here as those that have locally low abundances, make up a high proportion of assemblage species lists, understanding how the number of rare species within assemblages is changing will help elucidate patterns of recent biodiversity change. Here, we show that the number of rare species within assemblages is increasing, on average, across systems. This increase could arise in two ways: species already present in the assemblage decreasing in abundance but with no increase in extinctions, or additional species entering the assemblage in low numbers associated with an increase in immigration. The positive relationship between change in rarity and change in species richness provides evidence for the second explanation, i.e. higher net immigration than extinction among the rare species. These measurable changes in the structure of assemblages in the recent past underline the need to use multiple biodiversity metrics to understand biodiversity change.
Location and quantification of phosphorus and other elements in fully hydrated, soil-grown arbuscular mycorrhizas: a cryo-analytical scanning electron microscopy study.

• Concentrations of phosphorus (P), potassium (K), magnesium (Mg) and calcium (Ca) were determined in situ in fully hydrated arbuscular mycorrhizas by cryo-analytical scanning electron microscopy. The field- and glasshouse-grown plants (subterranean and white clovers, field pea and leek) were colonized by indigenous mycorrhizal fungi. • The [P] in intraradical hyphae was generally 60-170 mM, although up to 600 mM was recorded, and formed strong linear relationships with [K], up to 350 mM, and [Mg], up to 175 mM. Little Ca was detected. The turgid branches of young arbuscules contained 30-50 mM P, up to 100 mM K and little Mg. Collapsing arbuscule branches and clumped arbuscules had greatly elevated Ca (30-250 mM), but otherwise differed little from young arbuscule branches in elemental concentration. • The [P] was low or undetectable in 86% of uncolonized cortical cell vacuoles, but was generally elevated in vacuoles surrounding an arbuscule and in the liquid surrounding hyphae in intercellular spaces. • Our results suggest that both young arbuscules and intercellular hyphae are sites for P-transfer, that Mg2+ and K+ are probably balancing cations for P anions in hyphae, and that host cells may limit arbuscule lifespan through deposition of material rich in Ca.
Design Space Analysis for Cross-Point 1S1MTJ MRAM: Selector–MTJ Cooptimization

To increase the density of magnetoresistive random access memory (MRAM) beyond the 1T1MTJ MRAM cell in use today, the design space for 1S1MTJ MRAM array is analyzed by cooptimizing both selectors and MTJs. Current low-resistance MTJs for 1T1MTJ MRAM are not suitable for 1S1MTJ MRAM. Threshold-type selectors would induce a strong read disturb on the MTJ due to the snapback voltage (<inline-formula> <tex-math notation="LaTeX">${V}_{\mathrm {TH}}$ </tex-math></inline-formula>–<inline-formula> <tex-math notation="LaTeX">${V}_{\mathrm {HOLD}}$ </tex-math></inline-formula>) when the selector is turned on. Also, exponential-type selectors would degrade the read margin (RM) due to its large ON-state resistance. When using existing selectors to achieve a 1-M-bit 1S1MTJ array, it is necessary to adjust the product of resistance and area (RA) and the diameter of the MTJ. An MTJ with the RA <inline-formula> <tex-math notation="LaTeX">$= 15\,\,\Omega \cdot \mu \text{m}^{2}$ </tex-math></inline-formula> and the diameter = 50 nm can meet the criterion of RM > 10% for both exponential-type selectors (exponential slope = 300–500 mV/decade with the current density ~ 1 MA/cm<sup>2</sup>) and threshold-type selectors (<inline-formula> <tex-math notation="LaTeX">${V}_{\mathrm {TH}}$ </tex-math></inline-formula>–<inline-formula> <tex-math notation="LaTeX">${V}_{\mathrm {HOLD}} \sim ~250$ </tex-math></inline-formula> mV). A design space accommodating a selector variation of around 1% can be found for MTJs with tunnel magnetoresistance ratio (TMR) < 250%. With an increased TMR of 250%–350% of the MTJ, the tolerance of variations for exponential-type selectors and threshold-type selectors can be improved to 2% and 4%, respectively. This provides a chance for the 1S1MTJ MRAM with existing selectors.
Prefusion RSV F Immunization Elicits Th2-Mediated Lung Pathology in Mice When Formulated With a Th2 (but Not a Th1/Th2-Balanced) Adjuvant Despite Complete Viral Protection

Respiratory syncytial virus (RSV) remains the most common cause of lower respiratory tract infections in children worldwide. Development of a vaccine has been hindered by the risk of developing enhanced respiratory disease (ERD) upon natural exposure to the virus. Generation of higher quality neutralizing antibodies with stabilized pre-fusion F protein antigens has been proposed as a strategy to prevent ERD. We sought to test whether there was evidence of ERD in naïve BALB/c mice immunized with an unadjuvanted, stabilized pre-fusion F protein, and challenged with RSV line 19. We further sought to determine the extent to which formulation with a Th2-biased (alum) or a more Th1/Th2-balanced (Advax-SM) adjuvant influenced cellular responses and lung pathology. When exposed to RSV, mice immunized with pre-fusion F protein alone (PreF) exhibited increased airway eosinophilia and mucus accumulation. This was further exacerbated by formulation of PreF with Alum (aluminum hydroxide). Conversely, formulation of PreF with a Th1/Th2-balanced adjuvant, Advax-SM, not only suppressed RSV viral replication, but also inhibited airway eosinophilia and mucus accumulation. This was associated with lower numbers of lung innate lymphocyte cells (ILC2s) and CD4+ T cells producing IL-5+ or IL-13+ and increased IFNγ+ CD4+ and CD8+ T cells, in addition to RSV F-specific CD8+ T cells. These data suggest that in the absence of preimmunity, stabilized PreF antigens may still be associated with aberrant Th2 responses that induce lung pathology in response to RSV infection, and can be prevented by formulation with more Th1/Th2-balanced adjuvants that enhance CD4+ and CD8+ IFNγ+ T cell responses. This may support the use of stabilized PreF antigens with Th1/Th2-balanced adjuvants like, Advax-SM, as safer alternatives to alum in RSV vaccine candidates.
A Quantitative Modular Modeling Approach Reveals the Effects of Different A20 Feedback Implementations for the NF-kB Signaling Dynamics

Signaling pathways involve complex molecular interactions and are controled by non-linear regulatory mechanisms. If details of regulatory mechanisms are not fully elucidated, they can be implemented by different, equally reasonable mathematical representations in computational models. The study presented here focusses on NF-κB signaling, which is regulated by negative feedbacks via IκBα and A20. A20 inhibits NF-κB activation indirectly through interference with proteins that transduce the signal from the TNF receptor complex to activate the IκB kinase (IKK) complex. A number of pathway models has been developed implementing the A20 effect in different ways. We here focus on the question how different A20 feedback implementations impact the dynamics of NF-κB. To this end, we develop a modular modeling approach that allows combining previously published A20 modules with a common pathway core module. The resulting models are fitted to a published comprehensive experimental data set and therefore show quantitatively comparable NF-κB dynamics. Based on defined measures for the initial and long-term behavior we analyze the effects of a wide range of changes in the A20 feedback strength, the IκBα feedback strength and the TNFα stimulation strength on NF-κB dynamics. This shows similarities between the models but also model-specific differences. In particular, the A20 feedback strength and the TNFα stimulation strength affect initial and long-term NF-κB concentrations differently in the analyzed models. We validated our model predictions experimentally by varying TNFα concentrations applied to HeLa cells. These time course data indicate that only one of the A20 feedback models appropriately describes the impact of A20 on the NF-κB dynamics in this cell type.
Island-Style Monolithic Three-Dimensional CMOS-Nanoelectromechanical Logic Circuits

Island-style monolithic three-dimensional (M3D) CMOS- nanoelectromechanical (CMOS-NEM) reconfigurable logic (RL) circuits are experimentally demonstrated showing the full operation of the island-style RL: single-tile and tile-to-tile operation. For the fabrication of M3D CMOS-NEM RL circuits, 65-nm CMOS baseline process was used, in which copper NEM memory switches are integrated over the CMOS logic circuits by using dual damascene process. It is predicted that our proposed M3D CMOS-NEM RL circuits will exhibit <inline-formula> <tex-math notation="LaTeX">$4.6 \times$ </tex-math></inline-formula> higher chip density, <inline-formula> <tex-math notation="LaTeX">$2.3 \times$ </tex-math></inline-formula> higher operation frequency and <inline-formula> <tex-math notation="LaTeX">$9.3 \times$ </tex-math></inline-formula> lower power consumption than CMOS-only ones (tri-state buffer case) for tile-to-tile operation.
Magnitude of mesozooplankton variability: a case study from the Marginal Ice Zone of the Barents Sea in spring

Zooplankton was studied on eight stations in the marginal ice zone (MIZ) of the Barents Sea, in May 1999, along two transects across the ice edge. On each station, physical background measurements and zooplankton samples were taken every 6 h over a 24 h period at five discrete depth intervals. Cluster analysis revealed separation of open water stations from all ice stations as well as high similarity level among replicates belonging to particular station. Based on five replicates per station, analysis of variance (ANOVA) confirmed significant differences (P < 0.05) in abundances of the main mesozooplankton taxa among stations. Relations between the zooplankton community and environmental parameters were established using redundancy analysis (CANOCO). In total, 55% of mesozooplankton variability within studied area was explained by eight variables with significant conditional effects: depth stratum, fluorescence, temperature, salinity, bottom depth, latitude, bloom situation, and ice concentration. GLM models supported supposition about clear and negative relationship between concentration of Oithona similis, and overall mesozooplankton diversity. The analyses showed a dynamic relationship between mesozooplankton distribution and hydrological conditions on short-term scale. Furthermore, our study demonstrated that variability in the physical environment of dynamic MIZ of the Barents Sea has measurable effect on the Arctic pelagic ecosystem.
Nocardia pinensis sp. nov., an Actinomycete Found in Activated Sludge Foams in Australia

A new nocardioform actinomycete was isolated by filament micromanipulation during the course of a study into foaming in activated sludge plants in Australia. It constitutes the second most prevalent foaming organism in Australia after Nocardia amarae. These two foaming organisms can be differentiated morphologically, biochemically and chemotaxonomically. The microscopic appearance of the filaments of the new taxon resembles a pine tree. The filaments are Gram-positive, non-acid-fast, non-motile, non-sheathed and about 0·5-1·0 μm in diameter. On a complex medium, the colonies are orange, opaque, macroscopically dry and friable, microscopically moist and shiny, with a pasty texture and an entire edge. The strains are positive for catalase, oxidase and urease and are oxidative in their metabolism of glucose. No strain could degrade hypoxanthine, xanthine, tyrosine, casein, gelatin or aesculin and none could grow with lysozyme. The strains contain peptidoglycan type Aly, cell wall type IV, whole cell sugar pattern type A, phospholipid type PII, menaquinones ω-cyclo-MK-8 (H4), fatty acids comprising straight chain saturated and unsaturated acids and tuberculostearic acid, and mycolic acids with 58-64 carbons containing substantial amounts of unsaturated chains in the 2-position. The name Nocardia pinensis has been chosen for the new taxon because of the pine tree like appearance of the organism on microscopy. The type strain, UQM3063, is deposited at the University of Queensland, Department of Microbiology Culture Collection.
Model-Switching: Dealing with Fluctuating Workloads in Machine-Learning-as-a-Service Systems

Machine learning (ML) based prediction models, and especially deep neural networks (DNNs) are increasingly being served in the cloud in order to provide fast and accurate inferences. However, existing service ML serving systems have trouble dealing with fluctuating workloads and either drop re-quests or significantly expand hardware resources in response to load spikes. In this paper, we introduce Model-Switching, a new approach to dealing with fluctuating workloads when serving DNN models. Motivated by the observation that end-users of ML primarily care about the accuracy of responses that are returned within the deadline (which we refer to as effective accuracy), we propose to switch from complex and highly accurate DNN models to simpler but less accurate models in the presence of load spikes. We show that the flexibility introduced by enabling online model switching provides higher effective accuracy in the presence of fluctuating workloads compared to serving using any single model. We implement Model-Switching within Clipper, a state-of-art DNN model serving system, and demonstrate its advantages over baseline approaches.
Antimicrobial activity of some of the south-Indian spices against serotypes of Escherichia coli, Salmonella, Listeria monocytogenes and Aeromonas hydrophila

Antibacterial activity of extracts of Allium sativum (garlic), Myristica fragrans (nutmeg), Zingiber officinale (ginger), Allium cepa (onion) and Piper nigrum (pepper) has been evaluated against 20 different serogroups of Escherichia coli, 8 serotypes of Salmonella, Listeria monocytogenes and Aeromonas hydrophila. Garlic extract showed excellent antibacterial activity against all the test organisms, except L. monocytogenes. Nutmeg showed good anti-listerial activity, although activity against E. coli and Salmonella were serotype dependent. Both garlic and nutmeg extracts were effective against A. hydrophila. Extracts of ginger showed inhibitory activity against two serogroups of E. coli: as O8 (enterotoxigenic E. coli) and O88 only. Extracts of onion and pepper did not show any antibacterial activity against the test organisms.
Classification and Generation of Microscopy Images with Plasmodium Falciparum via Artificial Neural Networks

Background Recent studies use machine-learning techniques to detect parasites in microscopy images automatically. However, these tools are trained and tested in specific datasets. Indeed, even if over-fitting is avoided during the improvements of computer vision applications, large differences are expected. Differences might be related to settings of camera (exposure, white balance settings, etc) and different blood film slides preparation. Moreover, generative adversial networks offer new opportunities in microscopy: data homogenization, and increase of images in case of imbalanced or small sample size. Methods Taking into consideration all those aspects, in this paper, we describe a more complete view including both detection and generating synthetic images: i) an automated detection used to detect malaria parasites on stained blood smear images using machine learning techniques testing several datasets. ii) investigate transfer learning and further testing in different unseen datasets having different staining, microscope, resolution, etc. iii) a generative approach to create synthetic images which can deceive experts. Results The tested architecture achieved 0.98 and 0.95 area under the ROC curve in classifying images with respectively thin and thick smear. Moreover, the generated images proved to be very similar to the original and difficult to be distinguished by an expert microscopist, which identified correcly the real data for one dataset but had 50% misclassification for another dataset of images. Conclusion The proposed deep-learning architecture performed well on a classification task for malaria parasites classification. The automated detection for malaria can help the technician to reduce their work and do not need any presence of experts. Moreover, generative networks can also be applied to blood smear images to generate useful images for microscopists. Opening new ways to data augmentation, translation and homogenization.
The complex genomic basis of rapid convergent adaptation to pesticides across continents in a fungal plant pathogen

Convergent evolution leads to identical phenotypic traits in different species or populations. Convergence can be driven by standing variation allowing selection to favor identical alleles in parallel or the same mutations can arise independently. However, the molecular basis of such convergent adaptation remains often poorly resolved. Pesticide resistance in agricultural ecosystems is a hallmark of convergence in phenotypic traits. Here, we analyze the major fungal pathogen Zymoseptoria tritici causing serious losses on wheat and with parallel fungicide resistance emergence across continents. We sampled three population pairs each from a different continent spanning periods early and late in the application of fungicides. To identify causal loci for resistance, we combined knowledge from molecular genetics work and performed genome-wide association studies (GWAS) on a global set of isolates. We discovered yet unknown factors in azole resistance including membrane stability functions. We found strong support for the ‘hotspot’ model of resistance evolution with parallel changes in a small set of loci but additional loci showed more population-specific allele frequency changes. Genome-wide scans of selection showed that half of all known resistance loci were overlapping a selective sweep region. Hence, the application of fungicides was one of the major selective agents acting on the pathogen over the past decades. Furthermore, loci identified through GWAS showed the highest overlap with selective sweep regions underlining the importance to map phenotypic trait variation in evolving populations. Our population genomic analyses showed that both de novo mutations and gene flow likely contributed to the parallel emergence of resistance.