Miracle-dz/UniFAR-FTUs huggingface dataset:
Nitrification rates in two undisturbed tropical rain forests and three slash-and-burn sites of the Venezuelan Amazon

Nitrification was measured during the rainy season in two undisturbed tropical rain forests and three slash-and-burn sites in the Amazon region of southwestern Venezuela. Nitrification was higher in the soils of the slash-and-burn sites than in the undisturbed forests. Rates of nitrate production were 14.9 mg/kg/30 days in a forest on an Oxisol, 3.5 mg/kg/30 days in a forest on Ultisol, 23.2 mg/kg/30 days in a 1.5-yr-old slash-and-burn agricultural site on an Oxisol, 12.9 mg/kg/30 days in a 0.5-yr-old slashand-burn agricultural site on Ultisol, and 12.1 mg/kg/30 days in a 3.0-yr-old pasture on Ultisol. In the undisturbed forests, rates of nitrate production in the root mat averaged 93.5 mg/kg/30 days on Oxisols and 11.2 mg/kg/30 days on Ultisols. Nitrification rates dosely followed total nitrogen mineralization rates. Ammonium availability appears to regulate nitrification in both the undisturbed forests and in the slash-and-burn sites. Rates of nitrification in the undisturbed forests in this Amazon site on poor soils were lower than in other tropical forests on more nutrient rich soils.
Identificação e genotipagem de Mycobacterium bovis em bovinos positivos no teste intradérmico para tuberculose em Mato Grosso do Sul

Spoligotyping was performed in the present study to genotype Mycobacterium bovis isolates obtained from tissues of cattle that were positive in the comparative intradermal tuberculin test (CITT) in the state of Mato Grosso do Sul (Brazil). Tissue samples from 13 positive cattle from different municipalities of the state were cultured using a Stonebrink medium. The resulting colonies were subjected to Ziehl-Neelsen staining and all isolates exhibited the staining characteristics of AFB. The 13 isolates of AFB were identified by means of a multiplex PCR (mPCR) assay. The hsp65 gene was targeted for the identification of Mycobacterium spp. , whereas the IS6110 insertion sequence was targeted for the identification of the Mycobacterium tuberculosis complex (MTC) and the rvd1rv2031c region was explored for the detection of Mycobacterium bovis. The spoligotyping assay was performed to genotype mycobacterial isolates. Of the 13 cattle, seven had at least one lesion suggestive of tuberculosis in the retropharyngeal, parotid and lung lymph nodes or lung. The remaining six exhibited no lesions suggestive of the disease. In the mPCR, 11 of the 13 isolates (84.6%) were positive for Mycobacterium spp. , 8/13 (61.5%) were positive for the MTC and 7/13 (53.8%) were positive for M. bovis. Based on the spoligotyping, eight isolates were grouped into three different groups of genotypes and one isolate exhibited an orphan type. Four isolates exhibited spoligotype pattern SB0121, while two isolates were associated with the pattern SB1145, another two were associated with pattern SB0881 and one was associated with pattern SB0140. Spoligotyping confirmed the genetic diversity present among isolates found in the state of Mato Grosso do Sul. In addition, SB0121 was confirmed as the predominant profile.
Immiscible Rayleigh-Taylor turbulence using mesoscopic lattice Boltzmann algorithms

We studied turbulence induced by the Rayleigh-Taylor (RT) instability for 2D immiscible two-component flows by using a multicomponent lattice Boltzmann method with a Shan-Chen pseudopotential implemented on GPUs. We compare our results with the extension to the 2D case of the phenomenological theory for immiscible 3D RT studied by Chertkov and collaborators ({\it Physical Review E 71, 055301, 2005}). Furthermore, we compared the growth of the mixing layer, typical velocity, average density profiles and enstrophy with the equivalent case but for miscible two-component fluid. Both in the miscible and immiscible cases, the expected quadratic growth of the mixing layer and the linear growth of the typical velocity are observed with close long-time asymptotic prefactors but different initial transients. In the immiscible case, the enstrophy shows a tendency to grow like $\propto t^{3/2}$, with the highest values of vorticity concentrated close to the interface. In addition, we investigate the evolution of the typical drop size and the behavior of the total length of the interface in the emulsion-like state, showing the existence of a power law behavior compatible with our phenomenological predictions. Our results can also be considered as a first validation step to extend the application of lattice Boltzmann tool to study the 3D immiscible case.
Adversarial Shapley Value Experience Replay for Task-Free Continual Learning

Continual learning is a branch of deep learning that seeks to strike a balance between learning stability and plasticity. In this paper, we specifically focus on the task-free setting where data are streamed online without task metadata and clear task boundaries. A simple and highly effective algorithm class for this setting is known as Experience Replay (ER) that selectively stores data samples from previous experience and leverages them to interleave memory-based and online batch learning updates. Recent advances in ER have proposed novel methods for scoring which samples to store in memory and which memory samples to interleave with online data during learning updates. In this paper, we contribute a novel Adversarial Shapley value ER (ASER) method that scores memory data samples according to their ability to preserve latent decision boundaries for previously observed classes (to maintain learning stability and avoid forgetting) while interfering with latent decision boundaries of current classes being learned (to encourage plasticity and optimal learning of new class boundaries). Overall, we observe that ASER provides competitive or improved performance on a variety of datasets compared to state-of-the-art ER-based continual learning methods.
Gambaudo--Ghys construction on bounded cohomology

We consider a generalized Gambaudo--Ghys construction on bounded cohomology and prove its injectivity. As a corollary, we prove that the third bounded cohomology of the group of area-preserving diffeomorphisms on the 2-disc is infinite-dimensional. We also prove similar results for the case of the 2-sphere and the 2-torus.
Parallel One-Step Control of Parametrised Boolean Networks

Boolean network (BN) is a simple model widely used to study complex dynamic behaviour of biological systems. Nonetheless, it might be difficult to gather enough data to precisely capture the behavior of a biological system into a set of Boolean functions. These issues can be dealt with to some extent using parametrised Boolean networks (ParBNs), as this model allows leaving some update functions unspecified. In our work, we attack the control problem for ParBNs with asynchronous semantics. While there is an extensive work on controlling BNs without parameters, the problem of control for ParBNs has not been in fact addressed yet. The goal of control is to ensure the stabilisation of a system in a given state using as few interventions as possible. There are many ways to control BN dynamics. Here, we consider the one-step approach in which the system is instantaneously perturbed out of its actual state. A naïve approach to handle control of ParBNs is using parameter scan and solve the control problem for each parameter valuation separately using known techniques for non-parametrised BNs. This approach is however highly inefficient as the parameter space of ParBNs grows doubly exponentially in the worst case. We propose a novel semi-symbolic algorithm for the one-step control problem of ParBNs, that builds on symbolic data structures to avoid scanning individual parameters. We evaluate the performance of our approach on real biological models.
Forward modelling the multiwavelength properties of active galactic nuclei: application to X-ray and WISE mid-infrared samples

An empirical forward-modeling framework is developed to interpret the multiwavelength properties of Active Galactic Nuclei (AGN) and provide insights into the overlap and incompleteness of samples selected at different parts of the electromagnetic spectrum. The core of the model are observationally derived probabilites on the occupation of galaxies by X-ray selected AGN. These are used to seed mock galaxies drawn from stellar-mass functions with accretion events and then associate them with spectral energy distributions that describe both the stellar and AGN emission components. This approach is used to study the complementarity between X-ray and WISE mid-infrared AGN selection methods. We first show that the basic observational properties of the X-ray and WISE AGN (magnitude, redshift distributions) are adequately reproduced by the model. We then infer the level of contamination of the WISE selection and show that this is dominated by non-AGN at redshifts z < 0.5. These are star-forming galaxies that scatter into the WISE AGN selection wedge because of photometric uncertainties affecting their colours. Our baseline model shows a sharp drop in the number density of heavily obscured AGN above the Compton thick limit in the WISE bands. The model also overpredicts by a factor of 1.5 the fraction of X-ray associations in the WISE AGN selection box compared to observations. This suggests a population of X-ray faint sources that is not reproduced by the model. This discrepancy is discussed in the context of either heavily obscured or intrinsically X-ray weak AGN. Evidence is found in favour of the latter.
Structure, diversity and seasonal dynamics of algal communities, with special attention to diatoms, from “Lacul Dulce” (Lake no.3) – Turda (Cluj county, Romania)

Structure, diversity and seasonal dynamics of algal communities, with special attention to diatoms, from "Lacul Dulce" (Lake No. 3) -Turda (Cluj County, Romania). The subject of the present paper is the investigation of the algal communities inhabiting of Lake No. 3 (known as "Lacul Dulce") from Turda, Cluj County. The algal flora of this lake has not yet been investigated. There have been identified 80 algal taxa, belonging to 5 phyla: Cyanoprokaryota (12 taxa), Dinophyta (5 taxa), Bacillariophyta (48 taxa), Euglenophyta (9 taxa) and Chlorophyta (6 taxa). A special attention was paid to the investigation of diatom communities, the group of algae that is the subject of the first author's PhD thesis. The 48 identified diatoms belong to the following 7 families: Thalassiosiraceae, Chaetoceraceae, Fragilariaceae, Achnanthaceae, Naviculaceae, Bacillariaceae and Epithemiaceae. Some aspects regarding community structure, seasonal dynamics, ecological preferences (salinity concentration) were also studied and are discussed in the paper
Interaction of verapamil and halogenated inhalation anesthetics on hypoxic pulmonary vasoconstriction

Calcium channel blockers and halogenated inhalation anesthetics reduce hypoxic pulmonary vasoconstriction (HPV) when administered separately to isolated rat lungs. This study was undertaken to investigate the effect of combining the calcium channel blocker verapamil with halothane or isoflurane. HPV was elicited in three groups of experiments. First, we studied the effect of halothane 1.3 MAC and varying concentrations of verapamil. Halothane reduced HPV as a mean by 34.7%, and a dose–dependent reduction was seen with verapamil. The depressant effect of the combination of halothane and verapamil was significantly greater than when the drugs were administered alone. We further investigated in separate groups the effects of varying concentrations of halothane and isoflurane, administered both separately and in combination with a constant dose of verapamil (1.02 nmol). Both anesthetics depressed HPV in a dose–dependent fashion. Verapamil reduced HPV as a mean by 34.2% and 39.3% in the halothane and isoflurane groups, respectively. The inhibition caused by combining verapamil with an anesthetic was significantly greater than when administered separately. We conclude that verapamil in combination with halothane or isoflurane has an additive dampening effect on HPV.
Systematic comparison of deep belief network training using quantum annealing vs. classical techniques

In this work we revisit and expand on a 2015 study that used a D-Wave quantum annealer as a sampling engine to assist in the training of a Deep Neural Network. The original 2015 results were reproduced using more recent D-Wave hardware. We systematically compare this quantum-assisted training method to a wider range of classical techniques, including: Contrastive Divergence with a different choice of optimizer; Contrastive Divergence with an increased number of steps (CD-k); and Simulated Annealing (SA). We find that quantum-assisted training still outperforms the CD with Gibbs sampling-based techniques; however, SA is able to match the performance of quantum-assisted training trivially using a quench-like schedule with a single sweep at high temperature followed by one at the target temperature.
Web of the giant: Spectroscopic confirmation of a large-scale structure around the z = 6.31 quasar SDSS J1030+0524

We report on the spectroscopic confirmation of a large-scale structure around the luminous z = 6.31 quasi-stellar object (QSO) SDSS J1030+0524, powered by a one billion solar mass black hole. The structure is populated by at least six members, namely, four Lyman-break galaxies (LBGs), and two Lyman alpha emitters (LAEs). The four LBGs were identified among a sample of 21 i-band dropouts with zAB < 25.5 selected up to projected separations of 5 physical Mpc (15 arcmin) from the QSO. Their redshifts were determined through multi-object spectroscopic observations at 8−10 m class telescopes lasting up to eight hours. The two LAEs were identified in a 6 h VLT/MUSE observation centered on the QSO. The redshifts of the six galaxies cover the range between 6.129−6.355. Assuming that the peculiar velocities are negligible, this range corresponds to radial separations of ±5 physical Mpc from the QSO, that is comparable to the projected scale of the observed LBG distribution on the sky. We conservatively estimate that this structure is significant at a level > 3. 5σ and that the level of the galaxy overdensity is at least 1.5−2 within the large volume sampled (∼780 physical Mpc3). The spectral properties of the six member galaxies (Lyα strength and UV luminosity) are similar to those of field galaxies at similar redshifts. This is the first spectroscopic identification of a galaxy overdensity around a supermassive black hole in the first billion years of the Universe. Our finding lends support to the idea that the most distant and massive black holes form and grow within massive (>1012 M⊙) dark matter halos in large-scale structures and that the absence of earlier detections of such systems is likely due to observational limitations.
Boosting Share Routing for Multi-task Learning

Multi-task learning (MTL) aims to make full use of the knowledge contained in multi-task supervision signals to improve the overall performance. How to make the knowledge of multiple tasks shared appropriately is an open problem for MTL. Most existing deep MTL models are based on parameter sharing. However, suitable sharing mechanism is hard to design as the relationship among tasks is complicated. In this paper, we propose a general framework called Multi-Task Neural Architecture Search (MTNAS) to efficiently find a suitable sharing route for a given MTL problem. MTNAS modularizes the sharing part into multiple layers of sub-networks. It allows sparse connection among these sub-networks and soft sharing based on gating is enabled for a certain route. Benefiting from such setting, each candidate architecture in our search space defines a dynamic sparse sharing route which is more flexible compared with full-sharing in previous approaches. We show that existing typical sharing approaches are sub-graphs in our search space. Extensive experiments on three real-world recommendation datasets demonstrate MTANS achieves consistent improvement compared with single-task models and typical multi-task methods while maintaining high computation efficiency. Furthermore, in-depth experiments demonstrates that MTNAS can learn suitable sparse route to mitigate negative transfer.
Observational Constraints on the Physical Properties of Interstellar Dust in the Post-Planck Era

We present a synthesis of the astronomical observations constraining the wavelength-dependent extinction, emission, and polarization from interstellar dust from UV to microwave wavelengths on diffuse Galactic sight lines. Representative solid-phase abundances for those sight lines are also derived. Given the sensitive new observations of polarized dust emission provided by the Planck satellite, we place particular emphasis on dust polarimetry, including continuum polarized extinction, polarization in the carbonaceous and silicate spectroscopic features, the wavelength-dependent polarization fraction of the dust emission, and the connection between optical polarized extinction and far-infrared polarized emission. Together, these constitute a set of constraints that should be reproduced by models of dust in the diffuse interstellar medium.
Accounting for correlated horizontal pleiotropy in two-sample Mendelian randomization using correlated instrumental variants

Mendelian randomization (MR) is a powerful approach to examine the causal relationships between health risk factors and outcomes from observational studies. Due to the proliferation of genome-wide association studies (GWASs) and abundant fully accessible GWASs summary statistics, a variety of two-sample MR methods for summary data have been developed to either detect or account for horizontal pleiotropy, primarily based on the assumption that the effects of variants on exposure ({\gamma}) and horizontal pleiotropy ({\alpha}) are independent. This assumption is too strict and can be easily violated because of the correlated horizontal pleiotropy (CHP). To account for this CHP, we propose a Bayesian approach, MR-Corr2, that uses the orthogonal projection to reparameterize the bivariate normal distribution for {\gamma} and {\alpha}, and a spike-slab prior to mitigate the impact of CHP. We develop an efficient algorithm with paralleled Gibbs sampling. To demonstrate the advantages of MR-Corr2 over existing methods, we conducted comprehensive simulation studies to compare for both type-I error control and point estimates in various scenarios. By applying MR-Corr2 to study the relationships between pairs in two sets of complex traits, we did not identify the contradictory causal relationship between HDL-c and CAD. Moreover, the results provide a new perspective of the causal network among complex traits. The developed R package and code to reproduce all the results are available at this https URL.
Effect of different host plants on nutritional indices of wild silk moth, Cricula trifenestrata

Larvae of Cricula trifenestrata reared on Bakul showed the highest Consumption Index (CI) during fifth instar (66.19). Approximate digestibility (AD) values of the larvae were highest (67.74%) on Som during first instar. efficiency of conversion of digested food (eCD) and efficiency of conversion of ingested food (ECI) (42.32% and 16.00%, respectively) was highest on Som during fifth instar. Whole larval instars showed the highest ECI and ECD values on Som (18.76% and 48.38% respectively), and the lowest of both values on Bakul (ECI: 15.11% and ECD: 36.54%). The results of nutritional indices indicated that Som was the best suitable host for feeding of C. trifenestrata.
Amplitude analysis of the 
B+→D+D−K+
 decay

Results are reported from an amplitude analysis of the $B^+\to D^+D^-K^+$ decay. The analysis is carried out using LHCb proton-proton collision data taken at $\sqrt{s}=7,8,$ and $13$ TeV, corresponding to a total integrated luminosity of 9 fb$^{-1}$. In order to obtain a good description of the data, it is found to be necessary to include new spin-0 and spin-1 resonances in the $D^-K^+$ channel with masses around 2.9 GeV$/c^2$, and a new spin-0 charmonium resonance in proximity to the spin-2 $\chi_{c2}(3930)$ state. The masses and widths of these resonances are determined, as are the relative contributions of all components in the amplitude model, which additionally include the vector charmonia $\psi(3770)$, $\psi(4040)$, $\psi(4160)$ and $\psi(4415)$ states and a nonresonant component.
POSEIDON: Privacy-Preserving Federated Neural Network Learning

In this paper, we address the problem of privacy-preserving training and evaluation of neural networks in an $N$-party, federated learning setting. We propose a novel system, POSEIDON, the first of its kind in the regime of privacy-preserving neural network training, employing multiparty lattice-based cryptography and preserving the confidentiality of the training data, the model, and the evaluation data, under a passive-adversary model and collusions between up to $N-1$ parties. To efficiently execute the secure backpropagation algorithm for training neural networks, we provide a generic packing approach that enables Single Instruction, Multiple Data (SIMD) operations on encrypted data. We also introduce arbitrary linear transformations within the cryptographic bootstrapping operation, optimizing the costly cryptographic computations over the parties, and we define a constrained optimization problem for choosing the cryptographic parameters. Our experimental results show that POSEIDON achieves accuracy similar to centralized or decentralized non-private approaches and that its computation and communication overhead scales linearly with the number of parties. POSEIDON trains a 3-layer neural network on the MNIST dataset with 784 features and 60K samples distributed among 10 parties in less than 2 hours.
Design and Analysis of Switchback Experiments

Switchback experiments, where a firm sequentially exposes an experimental unit to random treatments, are among the most prevalent designs used in the technology sector, with applications ranging from ride-hailing platforms to online marketplaces. Although practitioners have widely adopted this technique, the derivation of the optimal design has been elusive, hindering practitioners from drawing valid causal conclusions with enough statistical power. We address this limitation by deriving the optimal design of switchback experiments under a range of different assumptions on the order of the carryover effect—the length of time a treatment persists in impacting the outcome. We cast the optimal experimental design problem as a minimax discrete optimization problem, identify the worst-case adversarial strategy, establish structural results, and solve the reduced problem via a continuous relaxation. For switchback experiments conducted under the optimal design, we provide two approaches for performing inference. The first provides exact randomization-based p-values, and the second uses a new finite population central limit theorem to conduct conservative hypothesis tests and build confidence intervals. We further provide theoretical results when the order of the carryover effect is misspecified and provide a data-driven procedure to identify the order of the carryover effect. We conduct extensive simulations to study the numerical performance and empirical properties of our results and conclude with practical suggestions. This paper was accepted by George Shanthikumar, big data analytics.