Miracle-dz/UniFAR-FTUs huggingface dataset:
Tansley Review No. 82. Strategies of arbuscular mycorrhizal fungi when infecting host plants

summary Arbuscular mycorrhizal (AM) fungi are ancient Zygomycetes, thought to have colonized the first land plants; today, they are associated with the roots of about 80% of plant species. The symbiosis they form is potentially valuable not only for developmental programmes based on low-input agriculture, but also as a complex experimental model, where both fungal and host plant growth are regulated. Here we review some recent progress m the area of cell and molecular biology of arbuscular mycorrhizas. Particular attention is given to strategies followed by AM fungi when, as obligate biotrophs, they establish a successful symbiosis with their host plants. Four topics are analysed: (i) parameters controlling fungal growth in the absence and presence of the host root, Le. events of DNA replication and timing of the cell cycle; (ii) mechanical and enzymatic mechanisms which allow the fungus to colonize root tissues, maintaining host viability; (iii) morphological changes induced by AM fungus host cells and, in particular, the formation de novo of a subcellular compartment termed the interface, and (iv) modifications of plant gene expression during fungal colonization, including those involving structural, symbiotic and defence-related genes.
Capacity for Seeding and Spreading of Argyrophilic Grain Disease in a Wild-Type Murine Model; Comparisons With Primary Age-Related Tauopathy

Argyrophilic grain disease (AGD) is a common 4R-tauopathy, causing or contributing to cognitive impairment in the elderly. AGD is characterized neuropathologically by pre-tangles in neurons, dendritic swellings called grains, threads, thorn-shaped astrocytes, and coiled bodies in oligodendrocytes in the limbic system. AGD has a characteristic pattern progressively involving the entorhinal cortex, amygdala, hippocampus, dentate gyrus, presubiculum, subiculum, hypothalamic nuclei, temporal cortex, and neocortex and brainstem, thus suggesting that argyrophilic grain pathology is a natural model of tau propagation. One series of WT mice was unilaterally inoculated in the hippocampus with sarkosyl-insoluble and sarkosyl-soluble fractions from “pure” AGD at the age of 3 or 7/12 months and killed 3 or 7 months later. Abnormal hyper-phosphorylated tau deposits were found in ipsilateral hippocampal neurons, grains (dots) in the hippocampus, and threads, dots and coiled bodies in the fimbria, as well as the ipsilateral and contralateral corpus callosum. The extension of lesions was wider in animals surviving 7 months compared with those surviving 3 months. Astrocytic inclusions were not observed at any time. Tau deposits were mainly composed of 4Rtau, but also 3Rtau. For comparative purposes, another series of WT mice was inoculated with sarkosyl-insoluble fractions from primary age-related tauopathy (PART), a pure neuronal neurofibrillary tangle 3Rtau + 4Rtau tauopathy involving the deep temporal cortex and limbic system. Abnormal hyper-phosphorylated tau deposits were found in neurons in the ipsilateral hippocampus, coiled bodies and threads in the fimbria, and the ipsilateral and contralateral corpus callosum, which extended with time along the anterior-posterior axis and distant regions such as hypothalamic nuclei and nuclei of the septum when comparing mice surviving 7 months with mice surviving 3 months. Astrocytic inclusions were not observed. Tau deposits were mainly composed of 4Rtau and 3Rtau. These results show the capacity for seeding and spreading of AGD tau and PART tau in the brain of WT mouse, and suggest that characteristics of host tau, in addition to those of inoculated tau, are key to identifying commonalities and differences between human tauopathies and corresponding murine models.
Mechanical and Material Tendon Properties in Patients With Proximal Patellar Tendinopathy

Introduction The effect of chronic patellar tendinopathy on tissue function and integrity is currently unclear and underinvestigated. The aim of this cohort comparison was to examine morphological, material, and mechanical properties of the patellar tendon and to extend earlier findings by measuring the ability to store and return elastic energy in symptomatic tendons. Methods Seventeen patients with chronic (>3 months, VISA-P < 80), inferior pole patellar tendinopathy (24 ± 4 years; male = 12, female = 5) were carefully matched to controls (25 ± 3 years) for training status, pattern, and history of loading of the patellar tendon. Individual knee extension force, patellar tendon stiffness, stress, strain, Young’s modulus, hysteresis, and energy storage capacity, were obtained with combined dynamometry, ultrasonography, magnetic resonance imaging, and electromyography. Results Anthropometric parameters did not differ between groups. VISA-P scores ranged from 28 to 78 points, and symptoms had lasted from 10 to 120 months before testing. Tendon proximal cross-sectional area was 61% larger in the patellar tendinopathy group than in the control group. There were no differences between groups in maximal voluntary isometric knee extension torque (p = 0.216; d < −0.31) nor in tensile tendon force produced during isometric ramp contractions (p = 0.185; d < −0.34). Similarly, tendon strain (p = 0.634; d < 0.12), hysteresis (p = 0.461; d < 0.18), and strain energy storage (p = 0.656; d < 0.36) did not differ between groups. However, patellar tendon stiffness (−19%; p = 0.007; d < −0.74), stress (−27%; p< 0.002; d < −0.90) and Young’s modulus (−32%; p = 0.001; d < −0.94) were significantly lower in tendinopathic patients compared to healthy controls. Discussion In this study, we observed lower stiffness in affected tendons. However, despite the substantial structural and histological changes occurring with tendinopathy, the tendon capacity to store and dissipate energy did not differ significantly.
Molecular comparison of prolate- and isometric-headed bacteriophages of lactococci

Twelve lytic phages that infect lactococci (eight prolate-headed and four isometric-headed phages) were compared via DNA–DNA hybridization, DNA restriction site mapping, genome size estimation, and analysis of virion proteins. Prolate-headed phages carried double-stranded DNA of 21.8 to 23.4 kilobases and showed three major virion proteins in SDS-polyacrylamide gel electrophoresis. Isometric-headed phages carried double-stranded DNA of 28.1 to 30.4 kilobases and showed one major virion protein. The DNA of all phages had cohesive ends. No DNA hybridization was observed between the two phage types. Restriction endonuclease cleavage site mapping of DNA showed similarities between some of the phages.Key words: Lactococcus lactis, bacteriophages, genome size, phage types, restriction site mapping.
Velocity-dependent self-interacting dark matter from groups and clusters of galaxies

We probe the self-interactions of dark matter with relaxed galaxy groups and clusters using observational data from strong and weak lensing and stellar kinematics. Our analysis uses the Jeans formalism and considers a wider range of systematic effects than in previous work, including adiabatic contraction and stellar anisotropy, to robustly constrain the self-interaction cross section. For both groups and clusters, our results show a mild preference for a nonzero cross section compared with cold collisionless dark matter. Our groups result, σ/m=0.5±0.2 cm2/g, places the first constraint on self-interacting dark matter (SIDM) at an intermediate scale M200∼ 1014 M⊙ between galaxies and massive clusters. For massive clusters with M200∼ 1015 M⊙, our result is σ/m=0.19±0.09 cm2/g, with an upper limit of σ / m < 0.35 cm2/g (95% CL) . Thus, our results disfavor a velocity-independent cross section of order 1 cm2/g or larger needed to impact small scale structure problems in galaxies, but are consistent with a velocity-dependent cross section that decreases with increasing scattering velocity. Comparing the cross sections with and without the effect of adiabatic contraction, we find that adiabatic contraction produces slightly larger values for our data sample, but they are consistent at the 1σ level. Finally, to validate our approach, we apply our Jeans analysis to a sample of mock data generated from SIDM-plus-baryons simulations with σ/m = 1 cm2/g. This is the first test of the Jeans model at the level of stellar and lensing observables directly measured from simulations. We find our analysis gives a robust determination of the cross section, as well as consistently inferring the true baryon and dark matter density profiles.
Effect of fungicides on the physiology of plants. Part IV: Protection of cellular organelles of senescent wheat leaves by carbendazim†

Wheat leaves (cv. Kormoran) floated on water and kept in darkness turned yellow. This induced senescence was accompanied by a loss of electrolytes and amino acids, and by disorganisation of all cellular organelles except cell walls. Treatment with a solution of carbendazim (20 μg ml−1) prevented the leakage of electrolytes and disorganisation of cell organelles. At 100 μg ml−1, the fungicide did not prevent the damage caused by senescence but stimulated the loss of electrolytes from the leaves. It is proposed that one of the major mechanisms of the antisenescent activity of carbendazim is its protective effect on membranes.
Effects of Artificial Shortening of the Photoperiod on Honeybee (Apis Mellifera) Polyethism

SummaryThe photoperiod was artificially shortened for free-flying honeybee colonies in May, June and July in order to simulate day-lengths of October, November and December. The effects on population development and on worker physiology were examined. There was no significant effect on numbers of brood cells or adult bees, or on the dry weight of the hypopharyngeal glands. The survival rates of workers did not increase significantly. On the other hand, the shortening of the photoperiod led to a winter-bee-like increase of the lipid and protein content of the fat body. However, the ‘short-day’ treatment was not enough to trigger the development of long-living winter bees.
Updated theoretical period–age and period–age–colour relations for Galactic Classical Cepheids: an application to the Gaia DR2 sample

Updated evolutionary and pulsational model predictions are combined in order to interpret the properties of Galactic Classical Cepheids in the Gaia Data Release 2. In particular, the location of the instability strip boundaries and the analytical relations connecting pulsation periods to the intrinsic stellar parameters are combined with evolutionary tracks to derive reliable and accurate period-age, and the first theoretical period-age-color relations in the Gaia bands for a solar chemical abundance pattern ($Z$=$0.02$, $Y$=$0.28$). The adopted theoretical framework takes into account possible variations in the mass-luminosity relation for the core helium-burning stage as due to changes in the core convective overshooting and/or mass loss efficiency, as well as the impact on the instability strip boundaries due to different assumptions for superadiabatic convection efficiency. The inferred period-age and period-age-color relations are applied to a selected sample of both fundamental and first overtone Gaia Cepheids, and individual ages for the various adopted theoretical scenarios are derived. The retrieved age distributions confirm that a variation in the efficiency of superadiabatic convection in the pulsational model computations has a negligible effect, whereas a brighter Mass-Luminosity relation, as produced by mild overshooting, rotation or mass loss, implies significantly older age predictions. Moreover, older Cepheids are found at larger Galactocentric distances, while first overtone Cepheids are found to be systematically older than the fundamental ones. The comparison with independent age distribution analysis in literature supports the predictive capability of current theoretical framework.
Real Time Speech Enhancement in the Waveform Domain

We present a causal speech enhancement model working on the raw waveform that runs in real-time on a laptop CPU. The proposed model is based on an encoder-decoder architecture with skip-connections. It is optimized on both time and frequency domains, using multiple loss functions. Empirical evidence shows that it is capable of removing various kinds of background noise including stationary and non-stationary noises, as well as room reverb. Additionally, we suggest a set of data augmentation techniques applied directly on the raw waveform which further improve model performance and its generalization abilities. We perform evaluations on several standard benchmarks, both using objective metrics and human judgements. The proposed model matches state-of-the-art performance of both causal and non causal methods while working directly on the raw waveform.
Effect of dietary supplementation of Azolla on growth and survibility of Labeo rohita fingerlings.

A feeding trial was conducted to study the effect of Azolla, on growth and survival of L. rohita fingerlings. One hundred twenty (4.08 ± 0.02 g) fingerlings were randomly distributed in four treatment groups, each with three replications. Four isonitrogenous (crude protein: 27.75-28.26%) experimental diets were prepared with different percentage of Azolla incorporation except the control group, viz., control (T 0 ), T 1 (20% Azolla), T 2 (40% Azolla) and T 3 (50% Azolla). The physio-chemical parameters were found in the normal range through out the experimental period. The results revealed that the test animals fed with diet containing 40 per cent Azolla showed better growth (15.45 ± 0.24 g in wt. and 13.73 ± 0.47 cm in length) than the test animals fed with 20 per cent, 50 per cent and control diet. The body weight gain per cent was recorded highest in diet containing 40 per cent Azolla (281.57 ± 7.21) than control (175.62 ± 2.31). The specific growth rate (SGR) was found highest in T 2 group (0.73 ± 0.01) followed by T 3 group (0.67± 0.01) which was (P < 0.05) higher than T 1 and control group. The FCR also varied significantly (P<0.05) among the treatment group. The better FCR was observed in T 2 group followed by T 3 group. This results suggest that incorporation of Azolla at 40 per cent can enhances growth in L. rohita fingerlings and can effectively be used in conventional diet of rohu without any adverse effect on growth and survival.
Does wildfire likelihood increase following insect outbreaks in conifer forests

Although there is acute concern that insect-caused tree mortality increases the likelihood or severity of subsequent wildfire, previous studies have been mixed, with findings typically based on stand-scale simulations or individual events. This study investigates landscape- and regional-scale wildfire likelihood following outbreaks of the two most prevalent native insect pests in the US Pacific Northwest (PNW): mountain pine beetle (MPB; Dendroctonus ponderosae) and western spruce budworm (WSB; Choristoneura freemani). We leverage seamless census data across numerous insect and fire events to (1) summarize the interannual dynamics of insects (1970–2012) and wildfires (1984–2012) across forested ecoregions of the PNW; (2) identify potential linked disturbance interactions with an empirical wildfire likelihood index; (3) quantify this insect-fire likelihood across different insect agents, time lags, ecoregions, and fire sizes. All three disturbance agents have occurred primarily in the drier, interior conif.
Distributional Individual Fairness in Clustering

In this paper, we initiate the study of fair clustering that ensures distributional similarity among similar individuals. In response to improving fairness in machine learning, recent papers have investigated fairness in clustering algorithms and have focused on the paradigm of statistical parity/group fairness. These efforts attempt to minimize bias against some protected groups in the population. However, to the best of our knowledge, the alternative viewpoint of individual fairness, introduced by Dwork et al. (ITCS 2012) in the context of classification, has not been considered for clustering so far. Similar to Dwork et al., we adopt the individual fairness notion which mandates that similar individuals should be treated similarly for clustering problems. We use the notion of $f$-divergence as a measure of statistical similarity that significantly generalizes the ones used by Dwork et al. We introduce a framework for assigning individuals, embedded in a metric space, to probability distributions over a bounded number of cluster centers. The objective is to ensure (a) low cost of clustering in expectation and (b) individuals that are close to each other in a given fairness space are mapped to statistically similar distributions. We provide an algorithm for clustering with $p$-norm objective ($k$-center, $k$-means are special cases) and individual fairness constraints with provable approximation guarantee. We extend this framework to include both group fairness and individual fairness inside the protected groups. Finally, we observe conditions under which individual fairness implies group fairness. We present extensive experimental evidence that justifies the effectiveness of our approach.
Changing protein profiles in developing and germinating barley seeds

Though useful information on barley proteins exists from earlier studies, present attempt represents a concerted study with added information on changing protein levels during seed development and seed germination. Albumins represen ted the major proteins at 4 daf and were overtaken by glutelins on further development. Glob ulins increased gradually to decline after 30 daf while prolamins which were low initially became second highest from 25 daf onward. New polypeptides were observed in globulin fraction eve n at 40 daf, no changes occurred in prolamin and glutelin fractions after 20 daf. The intensity of globulin polypeptides decreased after 30 daf and that of glutelin and prolamin polypeptides incr eased even till 45 daf. During germination, globulins degraded by 5 th day but their degradation products stayed even on 10 th day. Polypeptides in glutelin and prolamin fractions and their degradation products were not seen after 5 th day thus suggesting a relatively more fulfilling s torage role for these fractions. Degradation of Mr 62 kDa albumin polypeptide by 4 th day pointed towards its storage function. Similar trends followed by prolamins and glutelins during accumulation and degradation vis-avis by globulins warrant further work on their mole cular mechanisms and on relevance of such varying trends in barley seed biology.
Spin Relaxation Benchmarks and Individual Qubit Addressability for Holes in Quantum Dots

We investigate hole spin relaxation in the single- and multihole regime in a 2 × 2 germanium quantum dot array. We find spin relaxation times T1 as high as 32 and 1.2 ms for quantum dots with single- and five-hole occupations, respectively, setting benchmarks for spin relaxation times for hole quantum dots. Furthermore, we investigate qubit addressability and electric field sensitivity by measuring resonance frequency dependence of each qubit on gate voltages. We can tune the resonance frequency over a large range for both single and multihole qubits, while simultaneously finding that the resonance frequencies are only weakly dependent on neighboring gates. In particular, the five-hole qubit resonance frequency is more than 20 times as sensitive to its corresponding plunger gate. Excellent individual qubit tunability and long spin relaxation times make holes in germanium promising for addressable and high-fidelity spin qubits in dense two-dimensional quantum dot arrays for large-scale quantum information.
Critical adsorption of multiple polyelectrolytes onto a nanosphere: splitting the adsorption–desorption transition boundary

Employing extensive Monte Carlo computer simulations, we investigate in detail the properties of multichain adsorption of charged flexible polyelectrolytes (PEs) onto oppositely charged spherical nanoparticles (SNPs). We quantify the conditions of critical adsorption—the phase-separation curve between the adsorbed and desorbed states of the PEs—as a function of the SNP surface-charge density and the concentration of added salt. We study the degree of fluctuations of the PE–SNP electrostatic binding energy, which we use to quantify the emergence of the phase subtransitions, including a series of partially adsorbed PE configurations. We demonstrate how the phase-separation adsorption–desorption boundary shifts and splits into multiple subtransitions at low-salt conditions, thereby generalizing and extending the results for critical adsorption of a single PE onto the SNP. The current findings are relevant for finite concentrations of PEs around the attracting SNP, such as the conditions for PE adsorption onto globular proteins carrying opposite electric charges.
Perelomov-type coherent states of 
SO(D+1)
 in all-dimensional loop quantum gravity

A comprehensive study of the application of SO$(D+1)$ coherent states of Perelomov type to loop quantum gravity in general spacetime dimensions $D+1\geq 3$ is given in this paper. We focus on so-called simple representations of SO$(D+1)$ which solve the simplicity constraint and the associated homogeneous harmonic function spaces. With the harmonic function formulation, we study general properties of the coherent states such as the peakedness properties and the inner product. We also discuss the properties of geometric operators evaluated in the coherent states. In particular, we calculate the expectation value of the volume operator, and the results agree with the ones obtained from the classical label of the coherent states up to error terms which vanish in the limit of large representation labels $N$, i.e. the analogue of the large spin limit in standard $3+1$-dimensional loop quantum gravity.
Minimally critical endomorphisms of P^N

We study the dynamics of the map endomorphism of N-dimensional projective space defined by f(X)=AX^d, where A is a matrix and d is at least 2. When d>N^2+N+1, we show that the critical height of such a morphism is comparable to its height in moduli space, confirming a case of a natural generalization of a conjecture of Silverman.