Miracle-dz/UniFAR-FTUs huggingface dataset:
Distance as a Measure of Taxonomic Similarity

T HE, LAST FEW YEARS have seen the development of a number of methods for quantifying the classificatory process in systematics (Michener and Sokal, 1957; Sokal and Michener, 1958; Sokal, 1958; Sneath, 1957a; Sneath, 1957b, Cain and Harrison, 1958; Rogers and Tanimoto, 1960). These sudden developments, largely independently arrived at, appear to stem from, a growing dissatisfaction with the arbitrariness and subjectivity of the customary taxonomic procedure and would also appear to. be connected with the increasing availability of rapidmethods of data processing and computation. In spite of certain differences among them, these methods show substantial philosophical and procedural agreements. They call first of all for the computation of a measure of resemblance or similarity between taxa. Resemblances are computed between every pair of taxa in a given study and these resemblances are arranged in the form of a so-called Q-type matrix, which is a matrix of similarities among taxa. These matrices are subsequently analyzed by various types of clus-
Leaf production and curd initiation of winter cauliflower in response to temperature

SummaryIn experiments in 1994 and 1995 a range of transplanting dates and thermal crop covering treatments were used to produce different environmental conditions for the growth of two Roscoff cauliflower selections ‘December/January’ and ‘March’. In 1994 non-covered plants of ‘March’ initiated on average 19 d later and with 19 leaves more than ‘December/January’. In the two seasons, covering the crops gave delays in curd initiation of up to 93 d, depending on planting date, and increased the number of leaves produced by up to 50 compared with non-covered crops. Leaf production was best described by an accumulated effective day-degree scale using day-degrees <17°C for ‘December/ January’ and day-degrees <16°C for ‘March’. This shows that both light and temperature are concerned with controlling leaf production. During the juvenile phase of growth, apex diameters expanded linearly with temperature up to a diameter of about 0.2 mm. After this there was a different response to temperature suggesting that a p.
Optimizing BLE-Like Neighbor Discovery

Neighbor discovery (ND) protocols are used for establishing a first contact between multiple wireless devices. The energy consumption and discovery latency of this procedure are determined by the parametrization of the protocol. In most existing protocols, reception and transmission are temporally coupled. Such schemes are referred to as slotted, for which the problem of finding optimized parametrizations has been studied thoroughly in the literature. However, slotted approaches are not efficient in applications in which new devices join the network gradually and only the joining devices and a master node need to run the ND protocol simultaneously. For example, this is typically the case in IoT scenarios or bluetooth low energy (BLE) piconets. Here, slotless protocols that decouple reception and transmission can achieve significantly lower worst-case latencies than slotted ones. In this paper, we study slotless, BLE-like protocols, which schedule receptions and transmissions independently using periodic intervals (PI). For this class of protocols, optimal parameter values remain unknown. To address this, we propose an optimization framework for PI-based protocols, which translates any specified duty-cycle (and therefore energy budget) into a set of optimized parameter values. We show that the parametrizations resulting from one variant of our proposed scheme are optimal when one receiver discovers one transmitter, and no other parametrization or ND protocol – neither slotted nor slotless – can guarantee lower discovery latencies for a given duty-cycle in this scenario. Since the resulting protocol utilizes the channel more aggressively than other ND protocols, beacons will collide more frequently. Hence, due to collisions, the rate of successful discoveries gracefully decreases for larger numbers of devices discovering each other simultaneously. We also propose a scheme for configuring the BLE protocol (and not just BLE-like protocols). Though it is not clear whether the resulting parametrizations minimize the latencies of BLE, reasonably low worst-case latencies can be guaranteed.
Bright Optical Eigenmode of 1  nm^{3} Mode Volume.

We report on the discovery and rationale to devise bright single optical eigenmodes that feature quantum-optical mode volumes of about 1 nm^{3}. Our findings rely on the development and application of a quasinormal mode theory that self-consistently treats fields and electron nonlocality, spill-out, and Landau damping around atomistic protrusions on a metallic nanoantenna. By outpacing Landau damping with radiation via properly designed antenna modes, the extremely localized modes become bright with radiation efficiencies reaching 30% and could provide up to 4×10^{7} times intensity enhancement.
Ulva additions alter soil biogeochemistry and negatively impact Spartina alterniflora growth.

Although 2012 had a trend towards less biomass, the variability fell within the 95% confidence intervals. Additionally, examination of long term biomass and productivity from data from co-located plots suggest that while 2012 was lower than 2011, these years were not extremely different relative to long-term variability and trends. Error bars show SEM. In addition, no differences were found between 2011 and 2013 porewater nutrient data from co-located unfertilized plots.
Appendicular Myology of Kirtland's Warbler

KIRTLAND'S Warbler (Dendroica kirtlandii) is listed as one of the endangered species in the Red Book of Rare and endangered fish and wildlife of the United States (Goodwin et al., 1966). The total population of this warbler is about 1,000 birds (Mayfield, 1962). Inasmuch as the complete appendicular myology has not previously been described for any member of the family Parulidae, it seems worthwhile to describe and illustrate the myology of the Kirtland's Warbler. I am indebted to Robert W. Storer and Harrison B. Tordoff of the University of Michigan Museum of Zoology for one adult Kirtland's Warbler, collected in Montmorency County, Michigan, 26 June 1935, by Milton B. Trautman. Four other specimens were birds that I had hand-raised from the nest (Berger, 1966). I also acknowledge my appreciation to Mrs. Barbara Downs, who prepared the final ink drawings. Dissection under a binocular microscope is essential for the study of the myology of a bird the size of Kirtland's Warbler (approximately 53/4 inches in length). A few of the wing muscles and the short toe muscles approach the minimum size for description by means of gross dissection, even with magnifications X20 and X30. When studying a specimen of Fregilupus varius (Berger, 1957), I discovered by using histological techniques that M. latissimus dorsi pars posterior and M. abductor digiti IV were rudimentary muscles, consisting of a thin layer of striated fibers in a sheet of fascia. For all practical purposes, such a "muscle" is absent. The presence of rudimentary muscles may, however, be of special interest in certain studies, and the modified technique described by Berger (1956) is useful for making a quick preliminary determination of the presence of muscle fibers in fascia or ligament. The terminology of the muscles in this paper is that used by George and Berger (1966).
The Earth Mover's Correlation

Since Pearson's correlation was introduced at the end of the 19th century many dependence measures have appeared in the literature. Recently we have suggested four simple axioms for dependence measures of random variables that take values in Hilbert spaces. We showed that distance correlation satisfies all these axioms. We still need a new measure of dependence because existing measures either do not work in general metric spaces (that are not Hilbert spaces) or they do not satisfy our four simple axioms. The earth mover's correlation introduced in this paper applies in general metric spaces and satisfies our four axioms (two of them in a weaker form).
Traction Adaptive Motion Planning at the Limits of Handling

In this paper we address the problem of motion planning and control at the limits of handling, under locally varying traction conditions. We propose a novel solution method where locally varying traction is represented by time-varying tire force constraints. A constrained finite time optimal control problem is solved in a receding horizon fashion, imposing these time-varying constraints. Furthermore, we employ a sampling augmentation procedure to address the problems of infeasibility and sensitivity to local minima that arises when the constraint configuration is altered. We validate the proposed algorithm on a Volvo FH16 heavy-duty vehicle, in a range of critical scenarios. Experimental results indicate that traction adaptation improves the vehicle's capacity to avoid accidents, both when adapting to low and high local traction.
Deep Learning for Gravitational-Wave Data Analysis: A Resampling White-Box Approach

In this work, we apply Convolutional Neural Networks (CNNs) to detect gravitational wave (GW) signals of compact binary coalescences, using single-interferometer data from real LIGO detectors. Here, we adopted a resampling white-box approach to advance towards a statistical understanding of uncertainties intrinsic to CNNs in GW data analysis. We used Morlet wavelets to convert strain time series to time-frequency images. Moreover, we only worked with data of non-Gaussian noise and hardware injections, removing freedom to set signal-to-noise ratio (SNR) values in GW templates by hand, in order to reproduce more realistic experimental conditions. After hyperparameter adjustments, we found that resampling through repeated k-fold cross-validation smooths the stochasticity of mini-batch stochastic gradient descent present in accuracy perturbations by a factor of 3.6. CNNs are quite precise to detect noise, 0.952 for H1 data and 0.932 for L1 data; but, not sensitive enough to recall GW signals, 0.858 for H1 data and 0.768 for L1 data—although recall values are dependent on expected SNR. Our predictions are transparently understood by exploring tthe distribution of probabilistic scores outputted by the softmax layer, and they are strengthened by a receiving operating characteristic analysis and a paired-sample t-test to compare with a random classifier.
Development of a phosphorus index for pastures

Phosphorus (P) runoff from watersheds receiving animal manure applications is believed to be one of the most important contributing factors to eutrophication of nearby water bodies. Currently, state and federal agencies are proposing upper cutoff limits on soil test P, above which animal manures can no longer be applied, based on the assumption that high P concentrations in runoff are due to high soil test P levels. However, recent studies have shown that other factors may play a role in P runoff. Hence, the P Index (PT) was developed. One of the problems with the current P1 is that weighting factors for each of the variables affecting P runoff were based on professional opinion rather than data. The objective of this study was to modify and develop a P Index for pasture systems by evaluating several variables affecting P runoff. Treatments included: 1) effect of soil test P; 2) effect of soluble P in poultry litter; 3) effect of P in diet; 4) effect of fertilizer type; 5) effect of poultry litter application rate and 6) effect of application timing. Rainfall simulators were used to produce a 5 cm hr storm event on each scenario and P runoff was evaluated. Multiple regression was then used to analyze the data and determine the relative importance of each variable. Results showed that P runoff was most affected by the amount of soluble P in the fertilizer source, P application rates, and timing. Commercial P fertilizer resulted in the highest P runoff sue to high solubility. Results showed that soil test P had little effect on P runoff when animal manure was applied. Soluble runoff P concentrations increased with increasing fertilizer P solubility.
Systematic profiling of SARS-CoV-2 specific IgG epitopes at single amino acid resolution

SARS-CoV-2 specific IgG responses play critical roles for patients to recover from COVID-19, in-depth dissecting of the IgG responses on systems level is of great interest. Herein, we adopted a newly developed high-throughput epitope mapping technology (AbMap), analyzed 55 COVID-19 convalescent sera and 226 antibody samples enriched by specific proteins or peptides from these sera. We revealed three areas that are rich of IgG epitopes, two are on Spike protein but outside of RBD, and one is on Nucleocapsid protein. We identified 29 significant epitopes on Spike protein, from two of these significant epitopes, two critical epitope residues were found, i. e. , D936 and P1263, which are highly related to the infectivity of SARS-CoV-2. In summary, we provided the first global map of IgG binding epitopes for SARS-CoV-2 at single amino acid resolution. This map will facilitate the precise development of therapeutic antibodies and vaccines.
Central Yup'ik and Machine Translation of Low-Resource Polysynthetic Languages

Machine translation tools do not yet exist for the Yup'ik language, a polysynthetic language spoken by around 8,000 people who live primarily in Southwest Alaska. We compiled a parallel text corpus for Yup'ik and English and developed a morphological parser for Yup'ik based on grammar rules. We trained a seq2seq neural machine translation model with attention to translate Yup'ik input into English. We then compared the influence of different tokenization methods, namely rule-based, unsupervised (byte pair encoding), and unsupervised morphological (Morfessor) parsing, on BLEU score accuracy for Yup'ik to English translation. We find that using tokenized input increases the translation accuracy compared to that of unparsed input. Although overall Morfessor did best with a vocabulary size of 30k, our first experiments show that BPE performed best with a reduced vocabulary size.
UV upturn versus UV weak galaxies: differences and similarities of their stellar populations unveiled by a de-biased sample

The ultraviolet (UV) upturn is characterised by an unexpected up-rise of the UV flux in quiescent galaxies between the Lyman limit and 2500A. By making use of colour-colour diagrams, one can subdivide UV bright red-sequence galaxies in two groups: UV weak and upturn. With these two groups, we propose a comparison between their stellar population properties with the goal of establishing differences and similarities between them. We make use of propensity score matching (PSM) to mitigate potential biases between the two samples, by selecting similar objects in terms of redshift and stellar mass. Also, we take advantage of spectral energy distribution (SED) fitting results from magphys made available by the GAMA collaboration. The analyses are made by comparing the distributions from the SED fitting directly, as well as investigating the differences in correlations between their parameters, and finally by using principal component analysis (PCA). We explore important differences and similarities between UV weak and upturn galaxies in terms of several parameters, such as: metallicity, age, specific star formation rate, time of last burst of star-formation, to mention a few. Notable differences are those concerning (g-r) colour, metallicity, and time since last burst of star-formation: UV upturn are redder in the optical, more metallic, and their last burst of star-formation happened earlier in time. These differences suggest that UV upturn systems have shorter star-formation histories (i.e. have been evolving more passively) when compared to UV weak galaxies. Consequently, these last seem to have a higher diversity of stellar populations.
The MOSDEF survey: an improved Voronoi binning technique on spatially resolved stellar populations at z ∼ 2

We use a sample of 350 star-forming galaxies at 1.25 < z < 2.66 from the Multi-Object Spectrograph For Infra-Red Exploration (MOSFIRE) Deep Evolution Field survey to demonstrate an improved Voronoi binning technique that we use to study the properties of resolved stellar populations in z ∼ 2 galaxies. Stellar population and dust maps are constructed from the high-resolution CANDELS/3D-HST multiband imaging. Rather than constructing the layout of resolved elements (i.e. Voronoi bins) from the signal-to-noise (S/N) distribution of the H160-band alone, we introduce a modified Voronoi binning method that additionally incorporates the S/N distribution of several resolved filters. The spectral energy distribution (SED)-derived resolved E(B − V)stars, stellar population ages, star-formation rates (SFRs), and stellar masses that are inferred from the Voronoi bins constructed from multiple filters are generally consistent with the properties inferred from the integrated photometry within the uncertainties, with the exception of the inferred E(B − V)stars from our z ∼ 1.5 sample due to their UV slopes being unconstrained by the resolved photometry. The results from our multifilter Voronoi binning technique are compared to those derived from a ‘traditional’ single-filter Voronoi binning approach. We find that single-filter binning produces inferred E(B − V)stars that are systematically redder by 0.02 mag, on average, but could differ by up to 0.20 mag and could be attributed to poorly constrained resolved photometry covering the UV slope. Overall, we advocate that our methodology produces more reliable SED-derived parameters due to the best-fitting resolved SEDs being better constrained at all resolved wavelengths – particularly those covering the UV slope.
High Temperature Affects the Activity of Enzymes in the Committed Pathway of Starch Synthesis in Developing Wheat Endosperm

Ears of wheat were exposed for up to 10 days during the grain-filling stage to high temperature (35oC) and activities of five enzymes in the sucrose to starch pathway were compared to those in ears maintained at lower temperature (21oC day/16oC night). Two cultivars of wheat known to differ in their post-anthesis tolerance of high temperature were compared. On a per grain basis, the activity of sucrose synthase and of ADPglucose pyrophosphorylase in ears maintained at 21/16oC throughout did not change greatly between days 16 and 32 after anthesis, whereas UDPglucose pyrophosphorylase and soluble starch synthase activities declined with advancing development. Soluble starch synthase activity in grains of heated ears was decreased within 1 day to about one- half of the value in unheated grains, and 3 days' additional heating did not reduce the activity much further. Insoluble starch synthase activity was not significantly reduced by heating. Compared to soluble starch synthase, ADPglucose pyrophosphorylase activity was more slowly affected and decreased to a lesser extent by heat. Sucrose synthase and UDPglucose pyrophosphorylase activities were either not affected or only slightly reduced; part of this reduction could be due to advanced development at the higher temperature. In recovery experiments ears were heated for brief periods and then returned to 21/16oC for a few days. ADPglucose pyrophosphorylase and soluble starch synthase activities recovered in the cooler conditions but the other two enzymes generally only maintained or lost further activity. From a comparison of the activities of these enzymes with the rate of starch deposition, and by taking into account the effects of heating, it is proposed that the influence of heating on final grain dry weight is attributable to the observed reductions of soluble starch synthase activity.
Early galaxy growth: mergers or gravitational instability?

We investigate the spatially-resolved morphology of galaxies in the early Universe. We consider a typical redshift z = 6 Lyman Break galaxy, "Althaea" from the SERRA hydrodynamical simulations. We create mock rest-frame ultraviolet, optical, and far-infrared observations, and perform a two-dimensional morphological analysis to de-blend the galaxy disk from substructures (merging satellites or star-forming regions). We find that the [CII]158um emitting region has an effective radius 1.5 - 2.5 times larger than the optical one, consistent with recent observations. This [CII] halo in our simulated galaxy arises as the joint effect of stellar outflows and carbon photoionization by the galaxy UV field, rather than from the emission of unresolved nearby satellites. At the typical angular resolution of current observations (> 0.15") only merging satellites can be detected; detection of star-forming regions requires resolutions of 2 kpc, are merging satellites, rather than galactic substructures. Finally, the star-forming regions found in our mock maps follow the local L[CII] - SFR_UV relation of galaxy disks, although sampling the low-luminosity, low-SFR tail of the distribution. We show that future JWST observations, bridging UV and [CII] datasets, will be exceptionally suited to characterize galaxy substructures thanks to their exquisite spatial resolution and sensitivity to both low-metallicity and dust-obscured regions that are bright at infrared wavelengths.
Sparse or Dense: A Comparative Study of Code-Domain NOMA Systems

This paper is focused on code-domain non-orthogonal multiple access (CD-NOMA), which is an emerging paradigm to support massive connectivity for future machine-type wireless networks. We take a comparative approach to study two types of <italic>overloaded</italic> CD-NOMA, i.e., sparse code multiple access (SCMA) and dense code multiple access (DCMA), which are distinctive from each other in terms of their codebooks having <italic>sparsity</italic> or not. By analysing their individual diversity orders (DO) in Rayleigh fading channels, it is found that DCMA can be designed with the aid of generalized sphere decoder (i.e., a nonlinear multiuser detector) to enjoy full DO which is equal to the maximum number of resource nodes in the system. This is in contrast to SCMA whose error rate suffers from limited DO equal to the codebook sparsity (i.e., the effective number of resource nodes occupied by each user). We conduct theoretical analysis for the codebook design criteria and propose to use generalized sphere decoder for DCMA detection. We numerically evaluate two types of multiple access schemes under “<inline-formula> <tex-math notation="LaTeX">$4\times 6$ </tex-math></inline-formula>” (i.e., six users communicate over four subcarriers) and “<inline-formula> <tex-math notation="LaTeX">$5\times 10$ </tex-math></inline-formula>” NOMA settings and reveal that DCMA gives rise to significantly improved error rate performance in Rayleigh fading channels, whilst having decoding complexity comparable to that of SCMA.