Miracle-dz/UniFAR-FTUs huggingface dataset:
Multi-target integration and annotation of single-cell RNA-sequencing data

Cells are the building blocks of human tissues and organs, and the distributions of different cell-types change due to environmental or disease conditions and treatments. Single-cell RNA sequencing is used to study heterogeneity of cells in biological samples. To date, computational approaches aided in the discovery of dominant and rare cell-types and facilitated the construction of cell atlases. Integration of new data with the existing reference atlases is an emerging computational problem, and this paper proposes to frame it as a multi-target prediction task, solvable using supervised machine learning. We systematically and rigorously test 63 different predictors on synthetic benchmarks with different properties. The best performing predictor has high Cohen's Kappa scores and low mean absolute errors in single-batch and multi-batch integration experiments.
ROUTE FLOW ENTROPY MAXIMIZATION IN ORIGIN-BASED TRAFFIC ASSIGNMENT

This paper describes a new origin-based solution method for the static user-equilibrium traffic assignment problem. The implications of route flow entropy maximization are studied in the context of origin-based solutions. An alternative intuitive assumption is proposed, and the equivalence between the proposed assumption and the entropy maximization criterion is examined. As a result, a natural, easily obtainable route flow interpretation for origin-based solutions is derived. Related improvements to the origin-based solution method are discussed.
Numerical Analysis of the Interaction between Shallow （Square, Circular and Strip） Foundations and Subsoil

In this paper, the effects of the stiffness of circular, square and strip foundation structures and bonding effects were analyzed. Presented analysis was oriented on the influence of stiffness system “foundation—subsoil” and bonds (bi-directional bond and one-directional bond with and without friction). The results of numerical calculations have proved that the relative stiffness of system “foundation—subsoil” affect considerably the value and the distribution of contact stresses (vertical normal and shear stresses) in the foundation gap and value of the displacements (settlement, deflection and relative deformations) of foundation. From the numerical point of view, this problem was solved by deformation variant of the FEM (finite element method). The numerically obtained results were presented in the graphical and tabular forms. Obtained results were qualitative and quantitative compared with one another. From the calculation results it is obvious that relative stiffness of the system “foundation structure—subsoil” substantially affects distribution of contact stresses in the foundation subsoil and displacements (settlement, deflection and relative deformations, flexibility) of foundation. In the case of flexible foundations, the bond on the contact surfaces must be considered during the calculation. On the other hand, the effects of friction on the contact surface between the foundation and subsoil affect the distribution of contact stresses and deformations only to smaller extent.
Proton Modulation Near Solar Minimim Periods in Cosecutive Solar Cycles

Observations or the Pioneer/Voyager missions during 1985/1986/1987, together with observations at Earth in 1976/1977 and 1987, are compared with predictions of a steady-state modulation model. The qualitative features of the modulation are well understood, but to get quantitative agreement with observations, drastic modifications have to be made to the Parker spiral magnetic field above the solar poles.
SimilarityNet: A Deep Neural Network for Similarity Analysis Within Spatio‐temporal Ensembles

Latent feature spaces of deep neural networks are frequently used to effectively capture semantic characteristics of a given dataset. In the context of spatio‐temporal ensemble data, the latent space represents a similarity space without the need of an explicit definition of a field similarity measure. Commonly, these networks are trained for specific data within a targeted application. We instead propose a general training strategy in conjunction with a deep neural network architecture, which is readily applicable to any spatio‐temporal ensemble data without re‐training. The latent‐space visualization allows for a comprehensive visual analysis of patterns and temporal evolution within the ensemble. With the use of SimilarityNet, we are able to perform similarity analyses on large‐scale spatio‐temporal ensembles in less than a second on commodity consumer hardware. We qualitatively compare our results to visualizations with established field similarity measures to document the interpretability of our latent space visualizations and show that they are feasible for an in‐depth basic understanding of the underlying temporal evolution of a given ensemble.
Hybrid Touch/Tangible Spatial Selection in Augmented Reality

We study tangible touch tablets combined with Augmented Reality Head‐Mounted Displays (AR‐HMDs) to perform spatial 3D selections. We are primarily interested in the exploration of 3D unstructured datasets such as cloud points or volumetric datasets. AR‐HMDs immerse users by showing datasets stereoscopically, and tablets provide a set of 2D exploration tools. Because AR‐HMDs merge the visualization, interaction, and the users' physical spaces, users can also use the tablets as tangible objects in their 3D space. Nonetheless, the tablets' touch displays provide their own visualization and interaction spaces, separated from those of the AR‐HMD. This raises several research questions compared to traditional setups. In this paper, we theorize, discuss, and study different available mappings for manual spatial selections using a tangible tablet within an AR‐HMD space. We then study the use of this tablet within a 3D AR environment, compared to its use with a 2D external screen.
ModelWise: Interactive Model Comparison for Model Diagnosis, Improvement and Selection

Model comparison is an important process to facilitate model diagnosis, improvement, and selection when multiple models are developed for a classification task. It involves careful comparison concerning model performance and interpretation. Current visual analytics solutions often ignore the feature selection process. They either do not support detailed analysis of multiple multi‐class classifiers or rely on feature analysis alone to interpret model results. Understanding how different models make classification decisions, especially classification disagreements of the same instances, requires a deeper model understanding. We present ModelWise, a visual analytics method to compare multiple multi‐class classifiers in terms of model performance, feature space, and model explanation. ModelWise adapts visualizations with rich interactions to support multiple workflows to achieve model diagnosis, improvement, and selection. It considers feature subspaces generated for use in different models and improves model understanding by model explanation. We demonstrate the usability of ModelWise with two case studies, one with a small exemplar dataset and another developed with a machine learning expert with real‐world perioperative data.
Towards fluid force estimation of a water‐jetting aerial robot with hybrid kinematics‐force model

In this paper, a three‐dimensional hybrid kinematics‐force (HKF) model for fluid force estimation coupled with position optimization of an aerial robot capable of high‐pressure fluid ejection is presented. Motivated by the archerfish's unique (water‐jetting) hunting mechanics, the HKF model comprises of two sub‐models (hybrid kinematics and fluid force estimation) to maintain a specific fluid force at the point‐of‐contact (POC) during high altitude fluid jetting for high‐risk maintenance (cleaning) scenarios. Industries with high‐risk cleaning applications seek to employ robots to assist cleaners in routine operations on infrastructures or equipment at a height such as photovoltaic e‐glasses, impact‐sensitive objects, and many others. For a fluid jet, the stand‐off distance represents the length of the fluid trajectory between the nozzle orifice and POC, and is also a vital variable in fluid force control. If the stand‐off distance between the ejection source and the target is large, the fluid stream loses energy along the trajectory and the force at the POC is weakened thus losing some of the jet pressure at the target surface. The HKF model exploits this by estimating and maintaining a specific force at the POC through position optimization of the onboard nozzle coupled with the knowledge of the fluid parameters. To innovate high structure cleaning, the HKF model can be employed on an aerial robot with fluid ejection capabilities for accurate fluid force control at the POC. For high‐pressure fluid ejection (on horizontal and vertical structures), the HKF model is able to predict the (high pressure) fluid force at the POC with less than 10% error. The proposed HKF model is tested and verified through simulations and the experimentation results are validated by flying the physical prototypes in actual deployment scenarios.
University of Texas Radiocarbon Dates I

The C14 Dating Laboratory of the University of Texas has been working on the development of two systems of counting: gas counting with methane, and liquid scintillation counting with benzene. Lack of adequate instrumentation has retarded the work on gas counting, but the liquid scintillation work, supported in part by the Department of Chemistry, finally led to the successful development of a system in which the benzene counting solvent was synthesized from acetylene by pyrolysis (Tamers, Stipp, and Collier, 1961).
High-Precision 14C Measurement of Irish Oaks to Show the Natural 14C Variations from AD 1840 to 5210 BC

High-precision measurement of dendrochronologically dated Irish oak at bi-decade/decade intervals has continued in the Belfast laboratory, extending the 14C data base from ca AD 1840 to 5210 BC. The dendrochronology is now considered absolute (see Belfast dendrochronology this conference) (Brown et al, 1986) and a continuous detailed curve is presented, showing the natural variations in the atmospheric concentration of 14C over >7000 years. Each data point has a precision of <2.5. , and some 4500 years have now been compared with Seattle, giving excellent agreement. Discussion of this data base and the justification of the claimed accuracy is given together with a comparison of other chronologies. Some of the advantages and limitations of the above are discussed.
Verrucariaceae from Nepal

Abstract Twenty-eight species of Verrucariaceae are reported from Nepal. One genus and nine species are described as new: Nesothele gen. nov., sister to Staurothele s. lat. , with a crustose to squamulose thallus, hymenial algae and 4–8 colourless muriform ascospores per ascus; Nesothele glebulosa sp. nov., resembling N. rugulosa but with smaller perithecia; Thelidium uvidulum sp. nov., producing a thin thallus with soralia, prominent perithecia, and 1-septate ascospores; Verrucaria antepotens sp. nov., having a well-developed thallus with dark-sided areoles, immersed perithecia, and small ascospores 12.5–16.5 μm long; V. lactea sp. nov., resembling V. praetermissa but with larger ascospores and a strongly deviating ITS sequence; V. parvipeltata sp. nov., with brown, basally constricted areoles on an extensive dark prothallus; V. senta sp. nov., with a brown cracked thallus and prominent naked perithecia; Willeya eminens sp. nov., with prominent perithecia, and differing from W. protrudens in its ITS sequence; W. irrigata sp. nov. with a thallus cracked into dark-sided areoles, and relatively large ascospores 28.5–40 μm long; W. nepalensis sp. nov. with a cracked thallus, immersed perithecia and a distinctive ITS sequence. Three species complexes might contain new taxa, but wider geographical sampling is necessary before delimiting species: Thelidium minutulum, Verrucaria elaeomelaena and V. hydrophila. Five new combinations are made: Willeya honghensis comb. nov. (for Staurothele honghensis), Nesothele globosa comb. nov. (for Endocarpon globosum), N. hymenogonia comb. nov. (for Staurothele hymenogonia), N. rugulosa comb. nov. (for Staurothele rugulosa) and N. succedens comb. nov. (for Staurothele succedens). Four species are unidentified.
Cloning of the Coffea canephora SERK1 promoter and its molecular analysis during the cell-to-embryo transition

Background: Somatic embryogenesis receptor-like kinase 1 (SERK1) is a cell membrane receptor active in different plant tissues and involved in cell differentiation activities including somatic embryogenesis. The identification of promoter elements responsible for SERK1 expression during the onset of somatic embryogenesis can be useful to understand the molecular regulation of the cell-to embryo transition, and these promoter elements represent biotechnological tools in plant organ tissue culture. Results: A -1,620 bp DNA sequence located upstream of the Coffea canephora SERK1 gene homologue (CcSERK1) was isolated, and then, different segments containing key response elements (REs) for somatic embryogenesis onset and development were fused to the uidA (encoding a β-glucuronidase, GUS) reporter gene to evaluate its expression in transgenic leaf explants. DNA segments of -1,620 and -1048 bp in length directed uidA expression with patterns in leaf explants similar to those occurring during somatic embryogenesis. When a -792-bp fragment was used, uidA expression disappeared only in leaf explants and pro-embryogenic mass but persisted in developing embryos. No uidA expression was detected in any embryogenic stage when a -618-bp fragment was used. Conclusion: DNA deletions showed that a -1048-bp sequence located upstream of the CcSERK1 gene is sufficient to direct gene expression during the onset and the development of C. canephora somatic embryogenesis. The DNA segment located between -1048 and -792 bp (containing BBM and WUS REs) is needed for gene expression before embryogenesis onset but not during embryo development. The promoter segment between -792 and -618 bp (including GATA, ARR1AT, and ANT REs) regulates gene expression in developing embryos.
University of Bonn Natural Radiocarbon Measurements II

This list includes most of the dates produced from September 1967 to April 1968. The laboratory continues to use the benzene method of the previous date list (Radiocarbon, 1968, v. 10, p. 8–28); however, the counter and chemical treatment equipment were transferred to a field laboratory in order to avoid any possibility of contamination. Two new benzene synthesis lines of our own construction were added to the commercial unit. Their operation is excellent and over-all costs were nominal.
A Generalization of the Satisfiability Coding Lemma and Its Applications

The seminal Satisfiability Coding Lemma of Paturi, Pudlák, and Zane is a coding scheme for satisfying assignments of k -CNF formulas. We generalize it to give a coding scheme for implicants and use this generalized scheme to establish new structural and algorithmic properties of prime implicants of k -CNF formulas. Our first application is a near-optimal bound of n · 3 n (1 − Ω(1 /k )) on the number of prime implicants of any n -variable k -CNF formula. This resolves an open problem from the Ph.D. thesis of Talebanfard, who proved such a bound for the special case of constant-read k -CNF formulas. Our proof is algorithmic in nature, yielding an algorithm for computing the set of all prime implicants – the Blake Canonical Form – of a given k -CNF formula. The problem of computing the Blake Canonical Form of a given function is a classic one, dating back to Quine, and our work gives the first non-trivial algorithm for k -CNF formulas.
Prolegomena to a Middlebrow Arithmetic of Curves of Genus 2: Index rerum et personarum

Background and conventions 1. Curves of genus 2 2. Construction of the jacobian 3. The Kummer surface 4. The dual of the Kummer 5. Weddle's surface 6. G/2G 7. The jacobian over local fields Formal groups 8. Torsion 9. The isogeny Theory 10. The isogeny Applications 11. Computing the Mordell-Weil group 12. Heights 13. Rational points Chabauty's theorem 14. Reducible jacobians 15. The endomorphism ring 16. The desingularized Kummer 17. A neoclassical approach 18. Zukunftsmusik Appendix 1. MAPLE programs Appendix 2. Files available by FTP.
Quantum-Confinement Effect in Ultrathin Si Layer of Silicon-on-Insulator Substrate

We have studied the evolution of valence-band spectra during Si layer thinning in a silicon-on-insulator (SOI) substrate by X-ray photoelectron spectroscopy (XPS) in order to observe the quantum-confinement effect in two-dimensional Si. It was clearly observed that the valence-band maximum (VBM) shifts towards higher binding energies with decreasing Si thickness (< ∼10 nm). The VBM shifts were ascribed to vertical confinement of heavy holes in the quantum-well structure of a vacuum/single-crystalline Si/buried amorphous SiO2.
Collision-induced transport processes in planetary rings

The physics of collision-dominated particle disks around planets is analyzed from both the analytical and numerical point of view. The existence of Saturn's ringlet structure is analyzed in terms of a radial instability induced by viscous diffusion. The detailed model described is based on the assumption of uniform particle size. Modifications caused by finite particle size, gravitational effects, and a distribution of particle sizes are discussed.
Bayesian Non- and Semi-parametric Methods and Applications

This book reviews and develops Bayesian non-parametric and semi-parametric methods for applications in microeconometrics and quantitative marketing. Most econometric models used in microeconomics and marketing applications involve arbitrary distributional assumptions. As more data becomes available, a natural desire to provide methods that relax these assumptions arises. Peter Rossi advocates a Bayesian approach in which specific distributional assumptions are replaced with more flexible distributions based on mixtures of normals. The Bayesian approach can use either a large but fixed number of normal components in the mixture or an infinite number bounded only by the sample size. By using flexible distributional approximations instead of fixed parametric models, the Bayesian approach can reap the advantages of an efficient method that models all of the structure in the data while retaining desirable smoothing properties. Non-Bayesian non-parametric methods often require additional ad hoc rules to avoid “overfitting,” in which resulting density approximates are nonsmooth. With proper priors, the Bayesian approach largely avoids overfitting, while retaining flexibility. This book provides methods for assessing informative priors that require only simple data normalizations. The book also applies the mixture of the normals approximation method to a number of important models in microeconometrics and marketing, including the non-parametric and semi-parametric regression models, instrumental variables problems, and models of heterogeneity. In addition, the author has written a free online software package in R, “bayesm,” which implements all of the non-parametric models discussed in the book.
Effect of the Remnant Mass in Estimating the Stellar Mass of Galaxies

The definition of the galactic stellar mass estimated from the spectral energy distribution is ambiguous in the literature; whether the stellar mass includes the mass of the stellar remnants, i.e., white dwarfs, neutron stars, and black holes, is not well described. The remnant mass fraction in the total (living + remnant) stellar mass of a simple stellar population monotonically increases with the age of the population, and the initial mass function and metallicity affect the increasing rate. Since galaxies are composed of a number of stellar populations, the remnant mass fraction may depend on the total stellar mass of galaxies in a complex way. As a result, the shape of the stellar mass function of galaxies may change, depending on the definition of the stellar mass. In order to explore this issue, we ran a cosmological hydrodynamical simulation, and subsequently found that the remnant mass fraction indeed correlates with the total stellar mass of galaxies. However, this correlation is weak, and the remnant fraction can be regarded as a constant that depends only on the redshift. Therefore, the shape of the stellar mass function is almost unchanged, but it simply shifts horizontally if the remnant mass is included or not. The shift is larger at lower redshift, and it reaches 0.2-dex at z = 0 for a Chabrier IMF. Since this causes a systematic difference, we should take care of the definition of the ‘stellar’ mass, when comparing one’s result with others.
Narrowband Imaging in [O III] and Hα to Search for Intracluster Planetary Nebulae in the Virgo Cluster

We have identified intracluster planetary nebulae (PNs) in a Virgo Cluster core field by imaging with the Subaru Suprime-Cam through two narrowband filters centered at the redshifted wavelengths of the [O III] λ5007 and the Hα 6563 Å lines; broadband images in V and R were acquired to check for emission in the adjacent continuum. Emission-line objects in Virgo are then selected from the two-color diagram [O III]-Hα versus [O III]-(V+R), which is calibrated using PNs in M84 (Jacoby et al.). Using both [O III] and Hα allows us to distinguish bona fide planetary nebulae from high-redshift emission-line galaxies at the bright end of the [O III] luminosity function. Spectroscopic observations of a subsample of these objects were made at the Telescopio Nazionale Galileo and at the Very Large Telescope in a region around M84 and in an intracluster field, respectively. The observations confirm the efficiency of the combined [O III]+Hα imaging to identify true PNs. We also obtained the first spectrum of an intracluster PN that shows the [O III] doublet with a signal-to-noise ratio greater than 10 and its Hα emission. From the results based on the spectroscopic follow-up, we derive a lower limit to the fraction of the Virgo Cluster light contributed by the intracluster stars at the surveyed position in the cluster core: it amounts to 10%.
S0024282922000172jra 213..225

The epiphytic lichen species richness and community composition was compared for 600 living trees distributed within the interior of 60 Scots pine and Norway spruce monoculture stands in southern Sweden. A higher species richness, and more unique species, was found on trees of Scots pine than of Norway spruce, and distinctive communities were associated with the two tree species. Lichen species composition also shifted between the 30-, 55and 80-year-old stands, although there was no significant difference in species richness between the different age classes. Tree species and age of the stand explained most of the variation in community composition (41%), with additional variance explained by lichen proximity to the ground (6%) and aspect (1%) (northern/southern side of trunk). Scots pine and Norway spruce share many attributes, such as both being conifers with acidic bark properties and having a similar geographical distribution in Fennoscandia. However, our study showed that species richness and community composition can nevertheless diverge in stands dominated by these two tree species. Since the occurrence of red-listed species was low in these stands, we suggest that 80-year rotations are not long enough for the occurrence of the many rare and specialized lichen species that require old forest structures and long forest continuity in this region.