Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogenetically Structured Differences in rRNA Gene Sequence Variation among Species of Arbuscular Mycorrhizal Fungi and Their Implications for Sequence Clustering

ABSTRACT Arbuscular mycorrhizal (AM) fungi form mutualisms with plant roots that increase plant growth and shape plant communities. Each AM fungal cell contains a large amount of genetic diversity, but it is unclear if this diversity varies across evolutionary lineages. We found that sequence variation in the nuclear large-subunit (LSU) rRNA gene from 29 isolates representing 21 AM fungal species generally assorted into genus- and species-level clades, with the exception of species of the genera Claroideoglomus and Entrophospora. However, there were significant differences in the levels of sequence variation across the phylogeny and between genera, indicating that it is an evolutionarily constrained trait in AM fungi. These consistent patterns of sequence variation across both phylogenetic and taxonomic groups pose challenges to interpreting operational taxonomic units (OTUs) as approximations of species-level groups of AM fungi. We demonstrate that the OTUs produced by five sequence clustering methods using 97% or equivalent sequence similarity thresholds failed to match the expected species of AM fungi, although OTUs from AbundantOTU, CD-HIT-OTU, and CROP corresponded better to species than did OTUs from mothur or UPARSE. This lack of OTU-to-species correspondence resulted both from sequences of one species being split into multiple OTUs and from sequences of multiple species being lumped into the same OTU. The OTU richness therefore will not reliably correspond to the AM fungal species richness in environmental samples. Conservatively, this error can overestimate species richness by 4-fold or underestimate richness by one-half, and the direction of this error will depend on the genera represented in the sample. IMPORTANCE Arbuscular mycorrhizal (AM) fungi form important mutualisms with the roots of most plant species. Individual AM fungi are genetically diverse, but it is unclear whether the level of this diversity differs among evolutionary lineages. We found that the amount of sequence variation in an rRNA gene that is commonly used to identify AM fungal species varied significantly between evolutionary groups that correspond to different genera, with the exception of two genera that are genetically indistinguishable from each other. When we clustered groups of similar sequences into operational taxonomic units (OTUs) using five different clustering methods, these patterns of sequence variation caused the number of OTUs to either over- or underestimate the actual number of AM fungal species, depending on the genus. Our results indicate that OTU-based inferences about AM fungal species composition from environmental sequences can be improved if they take these taxonomically structured patterns of sequence variation into account.
Replacement Schemes and Two-Level Tables

This note completes the comparison of the performance of seven replacement schemes, as a function of the transposition-table size. A large number of chess middle-game and endgame positions has been studied. It turns out that the number of nodes of a subtree is a better estimate for potential savings than the depth of a subtree. A two-level table, using the number of nodes in the subtree searched as the deciding criterion, performs best and is recommended. Previous results based on fewer experiments are connrmed. 1 Background This note is a sequel to our previous article (Breuker et al., 1994) in which we compared the performance of seven replacement schemes on 18 middle-game positions. We then concluded that the number of nodes of a subtree is a better estimate of the work performed (and therefore potentially to be saved) than the depth of that subtree. Moreover, we arrived at the tentative conclusion that the traditional one-level implementation (one position per entry) was not the best. A two-level scheme, rst proposed by Ebeling (1986), seemed to work better. However, the observations were only based on 18 consecutive middle-game positions taken from one champion's game. Therefore, it was only a preliminary result we arrived at. 2 Experimental In this note the experiments are extended in two ways. The experiments are performed on 94 middle-game positions (including the 18 already tested), taken from six games between top-level Grandmasters. The experiments are conducted on 112 endgame positions 2 , taken from ve historic games between well-known chess (Grand)masters. The test positions are listed in the Appendix. In the experiments time stamping is used (Breuker et al., 1994). It only requires one additional bit per table position and requires little additional com-TwoBig1) have been tested on eight diierent table sizes, viz. from 8K to 1024K positions 3 , each time doubling the number of positions in the table. The middle-game positions have been searched 2 The endgame positions consist of positions both with and without blocked pawns. 3 K positions is equal to 1024 positions
What is the value of limited feedback for MIMO channels?

Feedback in a communications system can enable the transmitter to exploit channel conditions and avoid interference. In the case of a multiple-input multiple-output channel, feedback can be used to specify a precoding matrix at the transmitter, which activates the strongest channel modes. In situations where the feedback is severely limited, important issues are how to quantize the information needed at the transmitter and how much improvement in associated performance can be obtained as a function of the amount of feedback available. We give an overview of some recent work in this area. Methods are presented for constructing a set of possible precoding matrices, from which a particular choice can be relayed to the transmitter. Performance results show that even a few bits of feedback can provide performance close to that with full channel knowledge at the transmitter.
Herschel : the first science highlights Special feature L etter to the E ditor Deep Herschel view of obscured star formation in the Bullet cluster

We use deep, five band (100–500 μm) data from the Herschel Lensing Survey (HLS) to fully constrain the obscured star formation rate, SFRFIR, of galaxies in the Bullet cluster (z = 0.296), and a smaller background system (z = 0.35) in the same field. Herschel detects 23 Bullet cluster members with a total SFRFIR = 144 ± 14 M yr−1. On average, the background system contains brighter far-infrared (FIR) galaxies, with ∼50% higher SFRFIR (21 galaxies; 207±9 M yr−1). SFRs extrapolated from 24 μm flux via recent templates (SFR24 μm) agree well with SFRFIR for ∼60% of the cluster galaxies. In the remaining ∼40%, SFR24 μm underestimates SFRFIR due to a significant excess in observed S100/S24 (rest frame S75/S18) compared to templates of the same FIR luminosity.
Tight Bounds for Unconditional Authentication Protocols in the Manual Channel and Shared Key Models

We address the message authentication problem in two seemingly different communication models. In the first model, the sender and receiver are connected by an insecure channel and by a low-bandwidth auxiliary channel, that enables the sender to ldquomanuallyrdquo authenticate one short message to the receiver (for example, by typing a short string or comparing two short strings). We consider this model in a setting where no computational assumptions are made, and prove that for any there exists a -round protocol for authenticating -bit messages, in which only bits are manually authenticated, and any adversary (even computationally unbounded) has probability of at most to cheat the receiver into accepting a fraudulent message. Moreover, we develop a proof technique showing that our protocol is essentially optimal by providing a lower bound of on the required length of the manually authenticated string. The second model we consider is the traditional message authentication model. In this model, the sender and the receiver share a short secret key; however, they are connected only by an insecure channel. We apply the proof technique above to obtain a lower bound of on the required Shannon entropy of the shared key. This settles an open question posed by Gemmell and Naor (Advances in Cryptology-CRYPTO '93, pp. 355-367, 1993). Finally, we prove that one-way functions are necessary (and sufficient) for the existence of protocols breaking the above lower bounds in the computational setting.
THE FAR-INFRARED–RADIO CORRELATION AT HIGH REDSHIFTS: PHYSICAL CONSIDERATIONS AND PROSPECTS FOR THE SQUARE KILOMETER ARRAY

I present a predictive analysis for the behavior of the far-infrared (FIR)–radio correlation as a function of redshift in light of the deep radio continuum surveys which may become possible using the Square Kilometer Array (SKA). To keep a fixed ratio between the FIR and predominantly non-thermal radio continuum emission of a normal star-forming galaxy, whose cosmic-ray electrons typically lose most of their energy to synchrotron radiation and inverse Compton (IC) scattering, requires a nearly constant ratio between galaxy magnetic field and radiation field energy densities. While the additional term of IC losses off of the cosmic microwave background (CMB) is negligible in the local universe, the rapid increase in the strength of the CMB energy density (i.e., ∼(1 + z)4) suggests that evolution in the FIR–radio correlation should occur with infrared (IR; 8–1000 μm)/radio ratios increasing with redshift. This signature should be especially apparent once beyond z ∼ 3 where the magnetic field of a normal star-forming galaxy must be ∼50 μG to save the FIR–radio correlation. At present, observations do not show such a trend with redshift; z ∼ 6 radio-quiet quasars appear to lie on the local FIR–radio correlation while a sample of z ∼ 4.4 and z ∼ 2.2 submillimeter galaxies exhibit ratios that are a factor of ∼2.5 below the canonical value. I also derive a 5σ point-source sensitivity goal of ≈20 nJy (i.e., σrms ∼ 4 nJy) requiring that the SKA specified sensitivity be Aeff/Tsys ≈ 15, 000 m2 K−1; achieving this sensitivity should enable the detection of galaxies forming stars at a rate of ≳25 M☉ yr−1, such as typical luminous infrared galaxies (i.e., LIR ≳ 1011L☉), at all redshifts if present. By taking advantage of the fact that the non-thermal component of a galaxy's radio continuum emission will be quickly suppressed by IC losses off of the CMB, leaving only the thermal (free–free) component, I argue that deep radio continuum surveys at frequencies ≳10 GHz may prove to be the best probe for characterizing the high-z star formation history of the universe unbiased by dust.
Performance analysis of distributed symmetric sparse matrix vector multiplication algorithm for multi‐core architectures

Sparse matrix vector multiply (SpMVM) is an important kernel that frequently arises in high performance computing applications. Due to its low arithmetic intensity, several approaches have been proposed in literature to improve its scalability and efficiency in large scale computations. In this paper, our target systems are high end multi‐core architectures and we use messaging passing interface + open multiprocessing hybrid programming model for parallelism. We analyze the performance of recently proposed implementation of the distributed symmetric SpMVM, originally developed for large sparse symmetric matrices arising in ab initio nuclear structure calculations. We study important features of this implementation and compare with previously reported implementations that do not exploit underlying symmetry. Our SpMVM implementations leverage the hybrid paradigm to efficiently overlap expensive communications with computations. Our main comparison criterion is the ‘CPU core hours’ metric, which is the main measure of resource usage on supercomputers. We analyze the effects of topology‐aware mapping heuristic using simplified network load model. We have tested the different SpMVM implementations on two large clusters with 3D Torus and Dragonfly topology. Our results show that the distributed SpMVM implementation that exploits matrix symmetry and hides communication yields the best value for the ‘CPU core hours’ metric and significantly reduces data movement overheads. Copyright © 2015 John Wiley & Sons, Ltd.
On the Measurement of Polarisation: A Questionnaire Study

Starting from the axiomatisation of polarisation contained in Esteban and Ray (1994)and Chakravarty and Majumdar (2001) we investigate whether people's perceptionsof income polarisation is consistent with the key axioms. This is carried out using aquestionnaire-experimental approach that combines both paper questionnaires and onlineinteractive techniques. The responses suggest that important axioms which serveto differentiate polarisation from inequality - e.g. increased bipolarisation - as well asother distinctive features of polarisation, i.e. the non-monotonous behaviour attributedto polarisation, are not widely accepted.
Clitoral Priapism with No Known Risk Factors

Clitoral priapism is a rare condition that is associated with an extended duration of clitoral erection due to local engorgement of clitoral tissue resulting in pain. Although the pathophysiology is not completely understood, it has been associated with specific classes of medications, diseases that alter clitoral blood flow or others associated with small to large vessel disease. We present a case report of a 26-year-old patient who developed clitoral priapism without a clear medication or disease related etiology. The patient was treated with opiates, imipramine, non-steroidal anti-inflammatory medication, and local ice packs. She recovered uneventfully.
Primordial bispectrum from multifield inflation with nonminimal couplings

Realistic models of high-energy physics include multiple scalar fields. Renormalization requires that the fields have nonminimal couplings to the spacetime Ricci curvature scalar, and the couplings can be large at the energy scales of early-universe inflation. The nonminimal couplings induce a nontrivial field-space manifold in the Einstein frame, and they also yield an effective potential in the Einstein frame with nontrivial curvature. The ridges or bumps in the Einstein-frame potential can lead to primordial non-Gaussianities of observable magnitude. We develop a covariant formalism to study perturbations in such models and calculate the primordial bispectrum. As in previous studies of non-Gaussianities in multifield models, our results for the bispectrum depend sensitively on the fields’ initial conditions.
Shear-layer instability in a rotating system

The shear-layer instability in the flow over a rotating disk with a free surface is investigated experimentally by flow visualizations for a large range of the flow control parameters: the aspect ratio G of the cavity, the rotationnal Reynolds number Re and the radius ratio s between the inner and outer radii of the rotating disk. This instability develops along the cylindrical shroud as sharp-cornered polygonal patterns characterized by the number of vortices m. This number m can be scaled by considering an Ekman number based on the water depth, which confirms that the shroud boundary layer is of Stewartson type. The appearance threshold of the first polygonal mode is constant by considering the mixed Reynolds number introduced by Niino and Misawa (1984) based on both the water depth at rest and the rotating disk radius. For large values of s, the instability patterns appear along the hub as small stationary cells.
A rearrangeable algorithm for the construction of delay-constrained dynamic multicast trees

With the proliferation of multimedia group applications, the construction of multicast trees satisfying quality of service (QoS) requirements is becoming a problem of prime importance. Many of the multicast applications (such as video broadcasts and teleconferencing) require the network to support dynamic multicast sessions wherein the membership of the multicast group changes with time. We propose and evaluate an algorithm for on-line update of multicast trees to adjust to changes in group membership. The algorithm is based on a concept called quality factor (QF) that represents the usefulness of a portion of the multicast tree to the overall multicast session. When the usefulness of a particular region of the tree drops below a threshold, a rearrangement technique is used to suitably modify the tree. This algorithm aims to satisfy the delay-constraints of all current group members, at the same time minimizing the cost of the constructed tree. We compare the performance of our algorithm, by simulation, with that of an off-fine Steiner heuristic; with ARIES, a previously published algorithm for on-line update of unconstrained trees; and with the algorithm proposed by Hong, Lee and Park (see Proc. of IEEE INFOCOM, pp. 1433-40, 1998) for on-line update of delay-constrained trees. The simulation results indicate that our algorithm provides excellent cost-competitiveness that is better than that provided by the algorithm described by Hong et al., minimizes changes in the multicast tree after each update, and performs favorably even when compared with the unconstrained ARIES heuristic.
Mechanical characterisation of the human thoracic descending aorta: experiments and modelling

This work presents experiments and modelling aimed at characterising the passive mechanical behaviour of the human thoracic descending aorta. To this end, uniaxial tension and pressurisation tests on healthy samples corresponding to newborn, young and adult arteries are performed. Then, the tensile measurements are used to calibrate the material parameters of the Holzapfel constitutive model. This model is found to adequately adjust the material behaviour in a wide deformation range; in particular, it captures the progressive stiffness increase and the anisotropy due to the stretching of the collagen fibres. Finally, the assessment of these material parameters in the modelling of the pressurisation test is addressed. The implication of this study is the possibility to predict the mechanical response of the human thoracic descending aorta under generalised loading states like those that can occur in physiological conditions and/or in medical device applications.
ScienceDirect International Conference on Analytical Models and New Concepts in Concrete and Masonry Structures AMCM ’ 2017 Bond behavior of GRFP bars to concrete in beam test

Bond behavior between reinforcing bars and concrete is a key problem to understand behavior of reinforced concrete members. The introduction of the new reinforcing system made of fiber reinforced polymer (FRP) to construction industry forced the study of FRP-to-concrete bond behavior as one of the main mechanical properties. The application of FRP reinforcement in concrete structures increased rapidly in last years. Their excellent corrosion resistance, high tensile strength, good non-magnetic properties were the reason why they have become an alternative to traditional steel reinforcement, especially in harsh environments on bridges, outside garages and off-shore structures. The GFRP bars are very different from steel, mainly due to much lower elasticity modulus and their anisotropic structure. Good performance of FRP reinforced concrete requires adequate interfacial bond between bars and concrete, mainly due to surface preparation. The authors’ own experimental program includes twelve beam bond tests carried out on rectangular beams consisted of two concrete blocks connected by a continuous GFRP bar in tension and by a steel hinge in compression. Two main parameters were investigated in the tests: bar diameter and thickness of a bottom concrete cover. The GFRP bars indicated good bond behavior to concrete, mainly due to the ribs on the bar surface. The results of the test indicated the decrease in the ultimate shear bond stress with the increase in the bar diameter regardless of the thickness of the concrete cover. The decrease in the concrete cover caused the decrease in the shear bond stress for all bars diameters. The increase in bar diameter caused the decrease in the ultimate bond strength. © 2017 The Authors. Published by Elsevier Ltd. Peer-review under responsibility of the scientific committee of the International Conference on Analytical Models and New Concepts in Concrete and Masonry Structures.
Bromodeoxyuridine specifically labels the regenerative stem cells of planarians.

The singular regenerative abilities of planarians require a population of stem cells known as neoblasts. In response to wounding, or during the course of cell turnover, neoblasts are signaled to divide and/or differentiate, thereby replacing lost cell types. The study of these pluripotent stem cells and their role in planarian regeneration has been severely hampered by the reported inability of planarians to incorporate exogenous DNA precursors; thus, very little is known about the mechanisms that control proliferation and differentiation of this stem cell population within the planarian. Here we show that planarians are, in fact, capable of incorporating the thymidine analogue bromodeoxyuridine (BrdU), allowing neoblasts to be labeled specifically during the S phase of the cell cycle. We have used BrdU labeling to study the distribution of neoblasts in the intact animal, as well as to directly demonstrate the migration and differentiation of neoblasts. We have examined the proposal that a subset of neoblasts is arrested in the G2 phase of the cell cycle by double-labeling with BrdU and a mitosis-specific marker; we find that the median length of G2 (approximately 6 h) is sufficient to account for the initial mitotic burst observed after feeding or amputation. Continuous BrdU-labeling experiments also suggest that there is not a large, slow-cycling population of neoblasts in the intact animal. The ability to label specifically the regenerative stem cells, combined with the recently described use of double-stranded RNA to inhibit gene expression in the planarian, should serve to reignite interest in the flatworm as an experimental model for studying the problems of metazoan regeneration and the control of stem cell proliferation.