Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimal thinning of MCMC output

The use of heuristics to assess the convergence and compress the output of Markov chain Monte Carlo can be sub‐optimal in terms of the empirical approximations that are produced. Typically a number of the initial states are attributed to ‘burn in’ and removed, while the remainder of the chain is ‘thinned’ if compression is also required. In this paper, we consider the problem of retrospectively selecting a subset of states, of fixed cardinality, from the sample path such that the approximation provided by their empirical distribution is close to optimal. A novel method is proposed, based on greedy minimisation of a kernel Stein discrepancy, that is suitable when the gradient of the log‐target can be evaluated and approximation using a small number of states is required. Theoretical results guarantee consistency of the method and its effectiveness is demonstrated in the challenging context of parameter inference for ordinary differential equations. Software is available in the Stein Thinning package in Python, R and MATLAB.
DeepHist: Differentiable Joint and Color Histogram Layers for Image-to-Image Translation

We present the DeepHist - a novel Deep Learning framework for augmenting a network by histogram layers and demonstrate its strength by addressing image-to-image translation problems. Specifically, given an input image and a reference color distribution we aim to generate an output image with the structural appearance (content) of the input (source) yet with the colors of the reference. The key idea is a new technique for a differentiable construction of joint and color histograms of the output images. We further define a color distribution loss based on the Earth Mover's Distance between the output's and the reference's color histograms and a Mutual Information loss based on the joint histograms of the source and the output images. Promising results are shown for the tasks of color transfer, image colorization and edges $\rightarrow$ photo, where the color distribution of the output image is controlled. Comparison to Pix2Pix and CyclyGANs are shown.
Gas and dust cooling along the major axis of M 33 (HerM33es)

Context. M 33 is a gas rich spiral galaxy of the Local Group. Its vicinity allows us to study its interstellar medium (ISM) on linear scales corresponding to the sizes of individual giant molecular clouds. Aims. We investigate the relationship between the two major gas cooling lines and the total infrared (TIR) dust continuum. Methods. We mapped the emission of gas and dust in M 33 using the far-infrared lines of [C II] and [O I](63 μm) and the total infrared continuum. The line maps were observed with the PACS spectrometer on board the Herschel Space Observatory. These maps have 50 pc resolution and form a ∼370 pc wide stripe along its major axis covering the sites of bright H II regions, but also more quiescent arm and inter-arm regions from the southern arm at 2 kpc galacto-centric distance to the south out to 5.7 kpc distance to the north. Full-galaxy maps of the continuum emission at 24 μm from Spitzer/MIPS, and at 70 μm, 100 μm, and 160 μm from Herschel/PACS were combined to obtain a map of the TIR. Results. TIR and [C II] intensities are correlated over more than two orders of magnitude. The range of TIR translates to a range of far ultraviolet (FUV) emission of G0, obs ∼ 2 to 200 in units of the average Galactic radiation field. The binned [C II]/TIR ratio drops with rising TIR, with large, but decreasing scatter. The contribution of the cold neutral medium to the [C II] emission, as estimated from VLA H I data, is on average only 10%. Fits of modified black bodies to the continuum emission were used to estimate dust mass surface densities and total gas column densities. A correction for possible foreground absorption by cold gas was applied to the [O I] data before comparing it with models of photon dominated regions. Most of the ratios of [C II]/[O I] and ([C II]+[O I])/TIR are consistent with two model solutions. The median ratios are consistent with one solution at n ∼ 2 × 102 cm−3, G0 ∼ 60, and a second low-FUV solution at n ∼ 104 cm−3, G0 ∼ 1.5. Conclusions. The bulk of the gas along the lines-of-sight is represented by a low-density, high-FUV phase with low beam filling factors ∼1. A fraction of the gas may, however, be represented by the second solution.
s−d
 model for local and nonlocal spin dynamics in laser-excited magnetic heterostructures

We discuss a joint microscopic theory for the laser-induced magnetization dynamics and spin transport in magnetic heterostructures based on the s-d interaction. Angular momentum transfer is mediated by scattering of itinerant s electrons with the localized (d electron) spins. We use the corresponding rate equations and focus on a spin-12 d electron system, leading to a simplified analytical expression for the dynamics of the local magnetization that is coupled to an equation for the nonequilibrium spin accumulation of the s electrons. We show that this description converges to the microscopic three-temperature model in the limit of a strong s-d coupling. The equation for the spin accumulation is used to introduce diffusive spin transport. The presented numerical solutions show that during the laser-induced demagnetization in a ferromagnetic metal, a short-lived spin accumulation is created that counteracts the demagnetization process. Moreover, the spin accumulation leads to the generation of a spin current at the interface of a ferromagnetic and nonmagnetic metal. Depending on the specific magnetic system, both local spin dissipation and interfacial spin transport are able to enhance the demagnetization rate by providing relaxation channels for the spin accumulation that is built up during demagnetization in the ferromagnetic material.
Minimally Invasive Social Navigation

Integrating mobile robots into human society involves the fundamental problem of navigation in crowds. This problem has been studied by considering the behaviour of humans at the level of individuals, but this representation limits the computational efficiency of motion planning algorithms. We explore the idea of representing a crowd as a flow field, and propose a formal definition of path quality based on the concept of invasiveness; a robot should attempt to navigate in a way that is minimally invasive to humans in its environment. We develop an algorithmic framework for path planning based on this definition and present experimental results that indicate its effectiveness. These results open new algorithmic questions motivated by the flow field representation of crowds and are a necessary step on the path to end-to-end implementations.
Tree! I am no Tree! I am a Low Dimensional Hyperbolic Embedding

Given data, finding a faithful low-dimensional hyperbolic embedding of the data is a key method by which we can extract hierarchical information or learn representative geometric features of the data. In this paper, we explore a new method for learning hyperbolic representations that takes a metric-first approach. Rather than determining the low-dimensional hyperbolic embedding directly, we learn a tree structure on the data as an intermediate step. This tree structure can then be used directly to extract hierarchical information, embedded into a hyperbolic manifold using Sarkar's construction (Sarkar, 2012), or used as a tree approximation of the original metric. To this end, we present a novel fast algorithm TreeRep such that, given a $\delta$-hyperbolic metric (for any $\delta \geq 0$), the algorithm learns a tree structure that approximates the original metric. In the case when $\delta = 0$, we show analytically that TreeRep exactly recovers the original tree structure. We show empirically that TreeRep is not only many orders of magnitude faster than previous known algorithms, but also produces metrics with lower average distortion and higher mean average precision than most previous algorithms for learning hyperbolic embeddings, extracting hierarchical information, and approximating metrics via tree metrics.
Ringing of rotating black holes in higher-derivative gravity

We compute scalar quasinormal mode (QNM) frequencies in rotating black hole solutions of the most general class of higher-derivative gravity theories, to quartic order in the curvature, that reduce to General Relativity for weak fields and are compatible with its symmetries. The wave operator governing the QNMs is not separable, but we show one can extract the QNM frequencies by a projection onto the set of spheroidal harmonics. We have obtained accurate results for the quasinormal frequency corrections relative to Kerr for rotating black holes with dimensionless spins up to $\sim 0.7$. We also discuss to what extent our results carry over to the phenomenologically more relevant case of gravitational QNMs. Finally we provide an ancillary computational package that allows one to generalize our calculations to any effective energy-momentum tensor arising from higher-derivative terms in the effective action.
Seasonal radiation interception, dry matter production and yield determination for a semi-leafless pea (Pisum sativum) breeding selection under contrasting field conditions

SUMMARY Radiation interception, dry matter accumulation, flower and pod production and yield were measured for a semi-leafless pea (Pisum sativum) breeding selection (BS3) on three contrasting sites. Differences in soil moisture availability were largely responsible for a three-fold difference in yield between sites. Radiation interception was related to dry matter production by calculating photosynthetic efficiencies. In the absence of lodging, crop canopies converted intercepted radiation into dry matter with constant efficiency (ɛ) throughout the season; under conditions of moisture stress ɛ was reduced. Serious lodging during the post-flowering period on one site resulted in a mean seasonal photosynthetic efficiency (ɛ) 17% lower than ɛ. The ability of the pea crop canopy to intercept radiation was related also to yield components.
Lytic replication of Epstein-Barr virus

Epstein–Barr virus (EBV) is a gammaherpesvirus with a 172kb genome and many genes encoding enzymes for lytic viral DNA replication. Recent observations indicate that an S-phase-like environment and the activated DNA repair system are required for viral lytic DNA replication. The virally encoded DNA replication-associated enzymes are then expressed in two clusters, suggesting their participation at different stages of replication. Simultaneously, EBV-encoded regulatory proteins may modulate cell-cycle control to enhance virus replication efficiency. The interactions among proteins in the viral replication complex and cellular proteins may either generate structural specificities for replication proteins or stabilize the protein complexes. During infection, EBV has evolved several strategies to overcome the host defense mechanism, such as interfering with innate immunity and withdrawing into a latent state. This review discusses the latest progress in viral control of lytic replication and the interactions .
Calnexin Associates Exclusively with Individual CD3 and T Cell Antigen Receptor (TCR) Proteins Containing Incompletely Trimmed Glycans That Are Not Assembled into Multisubunit TCR Complexes (*)

Most T lymphocytes express on their surfaces an oligomeric protein complex consisting of clonotypic αβ polypeptides associated with invariant CD3- and chains, designated the T cell antigen receptor (TCR) complex. Assembly and intracellular transport of nascent TCR proteins is believed to be assisted by their interaction with the molecular chaperone calnexin, which for certain molecules functions as a lectin for monoglucosylated glycans. However, as most of our knowledge about calnexin-TCR protein associations has been obtained under conditions of limited TCR assembly, the role of calnexin in the formation of nascent TCR complexes is unclear. Here, we studied the role of glucose (Glc) trimming and calnexin association in the oligomerization of TCRα and CD3 glycoproteins in murine splenic T lymphocytes, a model cell type for efficient assembly of complete TCR complexes. We show that removal of Glc residues from both CD3 proteins and TCRα proteins occurred prior to their association with any other TCR components and that calnexin specifically interacted with unassembled TCRα and CD3 proteins containing incompletely trimmed oligosaccharides. Interestingly, we found that removal of Glc residues from glycan chains was necessary for efficient association of calnexin with TCRα glycoproteins but not with CD3 glycoproteins. These studies define Glc trimming and calnexin association as initial molecular events in the translation of CD3 and TCRα proteins, occurring coincident with or immediately after their translocation into the endoplasmic reticulum and preceding the ordered pairing of TCR chains. In addition, these data document that calnexin assembly with CD3 and TCRα glycoproteins involves both glycan-dependent and glycan-independent mechanisms.
Water Quality of the Canchim's Creek Watershed in São Carlos, SP, Brazil, Occupied by Beef and Dairy Cattle Activities

The Canchims creek watershed in Sao Carlos, SP, Brazil, was chosen to evaluate water quality affected by dairy and beef cattle production systems based on tropical pasture. The water samples were collected monthly, during three years, at six sampling points: spring in a tropical forest, spring in an intensive dairy production system, two dam springs, and stream water upward and at the delta. Results showed differences (P<0.01) among sampling points for the mean parameters. True color, hardness, turbidity, electric conductivity, alkalinity, pH, chemical oxygen demand and consumed oxygen explained well differences among sampling points. According to current legislation standards, water quality fitted with most of the established parameters for class 2, with exception of phosphate and iron. The high levels of total phosphorus, except in the forest spring, classified this water in an eutrophic class, even where soil and water conservation practices were considered adequate.
Does the systemic insecticide imidacloprid (Gaucho) have a direct effect on yield of grain sorghum

Gaucho 1 (imidacloprid; 1-[(6-chloro-3-pyridinyl)methyl]-N-nitro-2-imidazolidinimine) is a seed treatment insecticide widely used on sorghum [Sorghum bicolor (L.) Moench] to control a number of pests, including greenbugs [Schizaphis graminum (Rondani)], chinch bugs [Blissus leucopterus leucopterus (Say)], and wireworms (Limonius sp.). A series of tests was conducted at five locations in Kansas during 1996 and 1997 and three locations during 1998 to determine whether a yield response results even in the absence of pests when Gaucho is used as a seed treatment on grain sorghum. Results varied. Gaucho improved yields at Hesston, especially in the June plantings but some hybrids benefited more than others. These differences may have been due to chinch bugs that were observed in the plots and were known to be troublesome in the area. Because their numbers were low, other factors may have played a role. At the other locations and in the absence of chinch bugs, Gaucho had less of an influence on yields. At Garden City, where some greenbugs developed, Gaucho provided early-season control, but infestations were too light to influence yields. At Hays, Gaucho treatments appeared to have some influence on the numbers of corn earworms [Helicoverpa zea (Boddie)] in sorghum heads in one planting, although yield differences were not significant. Overall, this study found no consistent yield increases in fields treated with Gaucho in the absence of observable pest activity.
Heterosis and combining ability of CIMMYT's quality protein maize germplasm. II. Subtropical

Information on the combining ability and heterotic patterns of CIMMYT's maize (Zea mays L.) germplasm is of great value to maize breeders worldwide, for hybrid development. The objective of this study was to determine the heterosis and combining ability of CIMMYT's subtropical quality protein maize (QPM) germplasm, and to identify suitable germplasm for hybrid development. Six QPM gene pools and four QPM populations were used to make a 10-parent diallel. Parents and the 45 crosses were tested in three environments in Mexico and three in the USA (.)
The Effect of Economic Thresholds and Life-History Parameters on the Evolution of Pesticide Resistance in a Regional Setting

We explore the dynamics of alleles conferring insecticide resistance in agroecosystems in which economic thresholds are used to manage insect pest populations. The dynamics of economic thresholds on resistance evolution are first explored in a single-field model. A two-dimensional cellular automata model is then used to examine the effects of migration, refuges, and crop rotation in a large region of fields under different management strategies. The single-field model indicates that economic thresholds may have important implications for pesticide management strategies, because resistance evolution is no longer independent of the growth process. In the regional model, the growth rate of the population, the selection pressure on the resistant allele, and migration all affect the time to resistance. Rotation is most beneficial when migration rates are either very high or very low and has little effect at intermediate migration rates. Resistance develops in large patches, so the level of resistance in a given field may be only weakly related to the history of pesticide treatment in that field. This finding may explain the high regional variability found in field studies of resistance in pests such as Colorado potato beetle.
Evaluating Transmission Heterogeneity and Super-Spreading Event of COVID-19 in a Metropolis of China

Background: COVID-19 caused rapid mass infection worldwide. Understanding its transmission characteristics including heterogeneity is of vital importance for prediction and intervention of future epidemics. In addition, transmission heterogeneity usually envokes super spreading events (SSEs) where certain individuals infect large numbers of secondary cases. Till now, studies of transmission heterogeneity of COVID-19 and its underlying reason are far from reaching an agreement. MethodsWe collected information of all infected cases between January 21 and February 26, 2020 from official public sources in Tianjin, a metropolis of China. Utilizing a heterogeneous transmission model based on branching process along with a negative binomial offspring distribution, we estimated the reproductive number R and the dispersion parameter k which characterized the transmission potential and heterogeneity, respectively. Furthermore, we studied the SSE in Tianjin outbreak and evaluated the effect of control measures undertaken by local government based on the heterogeneous model. Results: A total of 135 confirmed cases (including 34 imported cases and 101 local infections) in Tianjin by February 26th 2020 entered the study. We grouped them into 43 transmission chains with the largest chain of 45 cases and the longest chain of 4 generations. The estimated reproduction number R was at 0.67 (95%CI: 0.54[~]0.84), and the dispersion parameter k was at 0.25 (95% CI: 0.13[~]0.88). A super spreader causing six infections in Tianjin, was identified. In addition, our simulation results showed that the outbreak in Tianjin would have caused 165 infections and sustained for 7.56 generations on average if no control measures had been taken by local government since January 28th. Conclusions: Our analysis suggested that the transmission of COVID-19 was subcritical but with significant heterogeneity and may incur SSE. More efforts are needed to verify the transmission heterogeneity of COVID-19 in other populations and its contributing factors, which is important for developing targeted measures to curb the pandemic.
Effects of Regulatory Network Organization and Environment on PmrD Connector Activity and Polymyxin Resistance in Klebsiella pneumoniae and Escherichia coli

Polymyxins are a class of cyclic peptides with antimicrobial activity against Gram-negative bacteria. In Enterobacteriaceae, the PhoQ/PhoP and PmrB/PmrA two-component systems regulate many genes that confer resistance to both polymyxins and host antimicrobial peptides. ABSTRACT Polymyxins are a class of cyclic peptides with antimicrobial activity against Gram-negative bacteria. In Enterobacteriaceae, the PhoQ/PhoP and PmrB/PmrA two-component systems regulate many genes that confer resistance to both polymyxins and host antimicrobial peptides. The activities of these two-component systems are modulated by additional proteins that are conserved across Enterobacteriaceae, such as MgrB, a negative regulator of PhoQ, and PmrD, a “connector” protein that activates PmrB/PmrA in response to PhoQ/PhoP stimulation. Despite the conservation of many protein components of the PhoQ/PhoP-PmrD-PmrB/PmrA network, the specific molecular interactions and regulatory mechanisms vary across different genera. Here, we explore the role of PmrD in modulating this signaling network in Klebsiella pneumoniae and Escherichia coli. We show that in K. pneumoniae, PmrD is not required for polymyxin resistance arising from mutation of mgrB—the most common cause of spontaneous polymyxin resistance in this bacterium—suggesting that direct activation of polymyxin resistance genes by PhoQ/PhoP plays a critical role in this resistance pathway. However, for conditions of low pH or intermediate iron concentrations, both of which stimulate PmrB/PmrA, we find that PmrD does contribute to resistance. We further show that in E. coli, PmrD functions as a connector between PhoQ/PhoP and PmrB/PmrA, in contrast with previous reports. In this case, activity also depends on PmrB/PmrA stimulation, or on very high activation of PhoQ/PhoP. Our results indicate that the importance of the PmrD connector in modulating the polymyxin resistance network depends on both the network organization and on the environmental conditions associated with PmrB stimulation.
Variation in the double-stranded RNA phenotype between and within different rust species

The dsRNA phenotype of 34 isolates representing 10 Australian pathotypes of Puccinia striiformis, 2 of P. recondita, and 1 each of P. graminis, P. sorghi, P. menthae, and Melampsora lini were examined. Each rust species had its own distinctive dsRNA pattern. Variation occurred in the dsRNA phenotype between the two isolates of P. recondita and among the 34 different isolates of P. striiformis but did not correlate with variation in pathotype. Single pustule isolates of P. graminis and P. recondita were examined to establish that all the dsRNAs were probably present in individual uredospores and were consistently transmitted asexually. The potential use of dsRNA phenotype as a cytoplasmic marker in rust population studies is discussed. Key words: dsRNA, Puccinia, rust.
Response to Comment on "Chromosomal Speciation and Molecular Divergence-Accelerated Evolution in Rearranged Chromosomes"

By clever use of outgroups, Lu et al . ([ 1 ][1]) tackle some of the questions raised by Navarro and Barton ([ 2 ][2]). Beyond confirming the previous result that rapidly evolving genes tend to be associated with chromosomes that have been rearranged between humans and chimpanzees ([ 2 ][2]), Lu et