Miracle-dz/UniFAR-FTUs huggingface dataset:
Deep Knowledge Tracing with Convolutions

Knowledge tracing (KT) has recently been an active research area of computational pedagogy. The task is to model students mastery level of knowledge based on their responses to the questions in the past, as well as predict the probabilities that they correctly answer subsequent questions in the future. A good KT model can not only make students timely aware of their knowledge states, but also help teachers develop better personalized teaching plans for students. KT tasks were historically solved using statistical modeling methods such as Bayesian inference and factor analysis, but recent advances in deep learning have led to the successive proposals that leverage deep neural networks, including long short-term memory networks, memory-augmented networks and self-attention networks. While those deep models demonstrate superior performance over the traditional approaches, they all neglect more or less the impact on knowledge states of the most recent questions answered by students. The forgetting curve theory states that human memory retention declines over time, therefore knowledge states should be mostly affected by the recent questions. Based on this observation, we propose a Convolutional Knowledge Tracing (CKT) model in this paper. In addition to modeling the long-term effect of the entire question-answer sequence, CKT also strengthens the short-term effect of recent questions using 3D convolutions, thereby effectively modeling the forgetting curve in the learning process. Extensive experiments show that CKT achieves the new state-of-the-art in predicting students performance compared with existing models. Using CKT, we gain 1.55 and 2.03 improvements in terms of AUC over DKT and DKVMN respectively, on the ASSISTments2009 dataset. And on the ASSISTments2015 dataset, the corresponding improvements are 1.01 and 1.96 respectively.
The Habitability of the Galactic Bulge

We present a new investigation of the habitability of the Milky Way bulge, that expands previous studies on the Galactic Habitable Zone. We discuss existing knowledge on the abundance of planets in the bulge, metallicity and the possible frequency of rocky planets, orbital stability and encounters, and the possibility of planets around the central supermassive black hole. We focus on two aspects that can present substantial differences with respect to the environment in the disk: (i) the ionizing radiation environment, due to the presence of the central black hole and to the highest rate of supernovae explosions and (ii) the efficiency of putative lithopanspermia mechanism for the diffusion of life between stellar systems. We use analytical models of the star density in the bulge to provide estimates of the rate of catastrophic events and of the diffusion timescales for life over interstellar distances.
Semantic based model of Conceptual Work Products for formal verification of complex interactive systems

Many clinical workflows depend on interactive computer systems for highly technical, conceptual work products, such as diagnoses, treatment plans, care coordination, and case management. We describe an automatic logic reasoner to verify objective specifications for these highly technical, but abstract, work products that are essential to care. The conceptual work products specifications serve as a fundamental output requirement, which must be clearly stated, correct and solvable. There is strategic importance for such specifications because, in turn, they enable system model checking to verify that machine functions taken with user procedures are actually able to achieve these abstract products. We chose case management of Multiple Sclerosis (MS) outpatients as our use case for its challenging complexity. As a first step, we illustrate how graphical class and state diagrams from UML can be developed and critiqued with subject matter experts to serve as specifications of the conceptual work product of case management. A key feature is that the specification must be declarative and thus independent of any process or technology. Our Work Domain Ontology with tools from Semantic Web is needed to translate UML class and state diagrams for verification of solvability with automatic reasoning. The solvable model will then be ready for subsequent use with model checking on the system of human procedures and machine functions. We used the expressive rule language SPARQL Inferencing Notation (SPIN) to develop formal representations of the UML class diagram, the state machine, and their interactions. Using SPIN, we proved the consistency of the interactions of static and dynamic concepts. We discussed how the new SPIN rule engine could be incorporated in the Object Management Group (OMG) Ontology Definition Metamodel (ODM)
International Winter Wheat Evaluation: Relationships among Test Sites Based on Cultivar Performance

Factor coefficients were correlated with location means for yield, heading and ripening dates, grain-fill duration, and winter survival. The correlations provided biological interpretations of groupings in terms of general stresses associated with winter wheat production. The relationships of international winter wheat test sites documented in this study should facilitate definition and understanding of regions of cultivar adaptation
A simplified parameterization of isoprene-epoxydiol-derived secondary organic aerosol (IEPOX-SOA) for global chemistry and climate models

Abstract. Secondary organic aerosol derived from isoprene epoxydiols (IEPOX-SOA) is thought to contribute the dominant fraction of total isoprene SOA, but the current volatility-based lumped SOA parameterizations are not appropriate to represent the reactive uptake of IEPOX onto acidified aerosols. A full explicit modelling of this chemistry is however computationally expensive owing to the many species and reactions tracked, which makes it difficult to include it in chemistry climate models for long-term studies. Here we present three simplified parameterizations for IEPOX-SOA simulation, based on an approximate analytical/fitting solution of the IEPOX-SOA yield and formation timescale. The yield and timescale can then be directly calculated using the global model fields of oxidants, NO, aerosol pH and other key properties, and dry deposition rates. The advantage of the proposed parameterizations is that they do not require the simulation of the intermediates while retaining the key physico-chemical dependencies. We have implemented the new parameterizations into the GEOS-Chem v11-02-rc chemical transport model, which has two empirical treatments for isoprene SOA (the volatility basis set (VBS) approach and a fixed 3 % yield parameterization) and compared all of them to the case with detailed full chemistry. The best parameterization (PAR3) captures the global tropospheric burden of IEPOX-SOA and its spatio-temporal distribution (R2 = 0.93) vs. those simulated by the full chemistry, while being more computationally efficient (~ 5 times faster), and accurately captures the response to changes on NOx and SO2 emissions. On the other hand, the constant 3 % yield that is now default in GEOS-Chem deviates strongly (R2 = 0.65, 63 % underestimation), as does the VBS (R2 = 0.45, 78 % underestimation), with neither parameterization capturing the response to emission changes. With the advent of new mass spectrometry instrumentation, many detailed SOA mechanisms are being developed, which will challenge global and especially climate models with their computational cost. The methods developed in this study can be applied to other SOA pathways, which can allow including accurate SOA simulations in climate and global modeling studies in the future.
Characterizing niche differentiation among marine consumers with amino acid δ13C fingerprinting

Abstract Marine food webs are highly compartmentalized, and characterizing the trophic niches among consumers is important for predicting how impact from human activities affects the structuring and functioning of marine food webs. Biomarkers such as bulk stable isotopes have proven to be powerful tools to elucidate trophic niches, but they may lack in resolution, particularly when spatiotemporal variability in a system is high. To close this gap, we investigated whether carbon isotope (δ13C) patterns of essential amino acids (EAAs), also termed δ13CAA fingerprints, can characterize niche differentiation in a highly dynamic marine system. Specifically, we tested the ability of δ13CAA fingerprints to differentiate trophic niches among six functional groups and ten individual species in the Baltic Sea. We also tested whether fingerprints of the common zooplanktivorous fishes, herring and sprat, differ among four Baltic Sea regions with different biochemical conditions and phytoplankton assemblages. Additionally, we investigated how these results compared to bulk C and N isotope data for the same sample set. We found significantly different δ13CAA fingerprints among all six functional groups. Species differentiation was in comparison less distinct, due to partial convergence of the species' fingerprints within functional groups. Herring and sprat displayed region‐specific δ13CAA fingerprints indicating that this approach could be used as a migratory marker. Niche metrics analyses showed that bulk isotope data had a lower power to differentiate between trophic niches than δ13CAA fingerprinting. We conclude that δ13CAA fingerprinting has a strong potential to advance our understanding of ecological niches, and trophic linkages from producers to higher trophic levels in dynamic marine systems. Given how management practices of marine resources and habitats are reshaping the structure and function of marine food webs, implementing new and powerful tracer methods are urgently needed to improve the knowledge base for policy makers.
Allelopathy and its coevolutionary implications between native and non‐native neighbors of invasive Cynara cardunculus L.

Abstract Invasive plants apply new selection pressures on neighbor plant species by different means including allelopathy. Recent evidence shows allelopathy functions as remarkably influential mediator for invaders to be successful in their invaded range. However, few studies have determined whether native and non‐native species co‐occurring with invaders have evolved tolerance to allelopathy. In this study, we conducted germination and growth experiments to evaluate whether co‐occurring native Juncus pallidus and non‐native Lolium rigidum species may evolve tolerance to the allelochemicals induced by Cyanara cardunculus in Australian agricultural fields. The test species were germinated and grown in pots filled with collected invaded and uninvaded rhizosphere soil of C. cardunculus with and without activated carbon (AC). Additionally, a separate experiment was done to differentiate the direct effects of AC on the test species. The soil properties showed invaded rhizosphere soils had higher total phenolic and lower pH compared with uninvaded soils. We found significant reduction of germination percentage and seedling growth in terms of above‐ and belowground biomass, and maximum plant height and root length of native in the invaded rhizosphere soil of C. cardunculus, but little effect on non‐native grass species. Even soil manipulated with AC showed no significant differences in the measured parameters of non‐native except aboveground biomass. Taken together, the results indicate allelochemicals induced by C. cardunculus exert more suppressive effects on native than non‐native linking the coevolved tolerance of those.
Rapid generation of ecologically relevant behavioral novelty in experimental cichlid hybrids

Abstract The East African cichlid radiations are characterized by repeated and rapid diversification into many distinct species with different ecological specializations and by a history of hybridization events between nonsister species. Such hybridization might provide important fuel for adaptive radiation. Interspecific hybrids can have extreme trait values or novel trait combinations and such transgressive phenotypes may allow some hybrids to explore ecological niches neither of the parental species could tap into. Here, we investigate the potential of second‐generation (F2) hybrids between two generalist cichlid species from Lake Malawi to exploit a resource neither parental species is specialized on: feeding by sifting sand. Some of the F2 hybrids phenotypically resembled fish of species that are specialized on sand sifting. We combined experimental behavioral and morphometric approaches to test whether the F2 hybrids are transgressive in both morphology and behavior related to sand sifting. We then performed a quantitative trait loci (QTL) analysis using RADseq markers to investigate the genetic architecture of morphological and behavioral traits. We show that transgression is present in several morphological traits, that novel trait combinations occur, and we observe transgressive trait values in sand sifting behavior in some of the F2 hybrids. Moreover, we find QTLs for morphology and for sand sifting behavior, suggesting the existence of some loci with moderate to large effects. We demonstrate that hybridization has the potential to rapidly generate novel and ecologically relevant phenotypes that may be suited to a niche neither of the parental species occupies. Interspecific hybridization may thereby contribute to the rapid generation of ecological diversity in cichlid radiations.
Effects of the fat-tailed ewes' body condition scores at lambing on their metabolic profile and offspring growth

Abstract This experiment aimed to evaluate the effect of body condition score (BCS) of fat-tailed Barbarine ewes at lambing on their metabolic profile around parturition and lamb's growth. The experiment was carried out on 69 Barbarine ewes, divided into three groups according to BCS, which were inferior to 2, between 2 and 2.5 and superior to 2.5 for the thin, middle and fat group, respectively. Along the trial, all groups received the same dietary treatment based on hay, pasture and concentrate. Birth weight (Bi-W), weights at 30 and 70 d (W30 and W70) and average daily gains (ADGs) of lambs were recorded. Metabolites were determined at late pregnancy and at the beginning of lactation. Ewes' BCS at lambing had no effect on lambs' Bi-W (P>0.05), which was 3.8, 3.8 and 3.9 kg, respectively, for thin, middle and fat groups. However, W30, W70 and ADG increased with a mother's BCS. A positive correlation between lamb growth parameters and ewe body weight and BCS at weaning was recorded. Energetic metabolites (glucose and triglycerides) and proteic metabolites (creatinine, total protein and urea) were similar among groups according to BCS but significantly different between pregnancy and lactation stages except triglycerides and urea. In conclusion, BCS may be used as dietary management tool during ewe lactation. With the transition from pregnancy to lactation, the content of some metabolites has changed irrespective of BCS; this aspect needs more investigations.
Genetic differentiation between two varieties of Oreocharis benthamii (Gesneriaceae) in sympatric and allopatric regions

Abstract The pattern of genetic differentiation between diverging species receives much attention as one of the key observable features of speciation. It has often been suggested that introgression between closely related species occurs commonly where their distributions overlap, leading to their becoming more morphologically and genetically similar, but there are a few opposite results. However, most of these studies have been carried out with animals and separate species; few have looked at intraspecific cases, especially in plants. Here, we conduct a comparative study on patterns of genetic differentiation among populations of two varieties of Oreocharis benthamii in allopatry and sympatry based on ISSR data for 754 individuals from 26 populations, in order to understand the processes leading to speciation. Contrary to expectations, the facultative xenogamy (mixed mating) species O. benthamii has a relatively low genetic diversity within populations (H = 0.1014, I = 0.1528) and high genetic differentiation among populations (G ST = 0.5867, ФST = 0.659), as is typically found for selfing species. Genetic variance between the two varieties in sympatric populations (44%, ФST = 0.444) is significantly more than that in allopatric populations (14%, ФST = 0.138). Consistent with the taxonomical delimitation of the two varieties, all sampled individuals of O. benthamii clustered into two genetic groups. Moreover, the genetic structures of populations of both varieties are correlated with their different geographical origins. Our studies show that significant divergence between sympatric populations of the two varieties could be attributed primarily to reinforcement by genetic divergent selection in sympatry where secondary contact had occurred. The major proportion of the genetic variation in outcrossing and mixed mating plants may exist among populations when the populations are distributed in fragmented habitats, due to the paucity of suitable habitat combined with inefficient seed dispersal mechanism and limited pollinator foraging area that may limit the gene flow.
Genetic evidence for sexual reproduction and multiple infections of Norway spruce cones by the rust fungus Thekopsora areolata

Abstract Rust fungi are obligate parasites, of plants, with complex and in many cases poorly known life cycles which may include host alteration and up to five spore types with haploid, diploid, and dikaryotic nuclear stages. This study supports that Thekopasora areolata, the causal agent of cherry‐spruce rust in Norway spruce, is a macrocyclic heteroecious fungus with all five spore stages which uses two host plants Prunus padus and Picea abies to complete its life cycle. High genotypic diversity without population structure was found, which suggests predominantly sexual reproduction, random mating and a high gene flow within and between the populations in Fennoscandia. There was no evidence for an autoecious life cycle resulting from aeciospore infection of pistillate cones that would explain the previously reported rust epidemics without the alternate host. However, within cones and scales identical multilocus genotypes were repeatedly sampled which can be explained by vegetative growth of the fertilized mycelia or repeated mating of mycelium by spermatia of the same genotype. The high genotypic diversity within cones and haplotype inference show that each pistillate cone is infected by several basidiospores. This study provides genetic evidence for high gene flow, sexual reproduction, and multiple infections of Norway spruce cone by the rust fungus T. areolata which expands the general understanding of the biology of rust fungi.
Surface stresses in complex viral capsids and non-quasi-equivalent viral architectures

Many larger and more complex viruses deviate from the capsid layouts predicted in the seminal Caspar–Klug theory of icosahedral viruses. Instead of being built from one type of capsid protein (CP), they code for multiple distinct structural proteins that either break the local symmetry of the CP building blocks (capsomers) in specific positions or exhibit auxiliary proteins that stabilize the capsid shell. We investigate here the hypothesis that this occurs as a response to mechanical stress. For this, we construct a coarse-grained model of a viral capsid, derived from the experimentally determined atomistic positions of the CPs, that represents the basic features of protein organization in the viral capsid as described in Caspar–Klug theory. We focus here on viruses in the PRD1-adenovirus lineage. For T = 28 viruses in this lineage, which have capsids formed from two distinct structural proteins, we show that the tangential shear stress in the viral capsid concentrates at the sites of local symmetry breaking. In the T = 21, 25 and 27 capsids, we show that stabilizing proteins decrease the tangential stress. These results suggest that mechanical properties can act as selective pressures on the evolution of capsid components, offsetting the coding cost imposed by the need for such additional protein components.
Variable Uptake of Selenium: Exposing Bryophytes in Situ to a Se-Gradient Watershed

Abstract. We investigated the uptake of selenium (Se) at 14 sites in a Se-rich watershed, using an aquatic bryophyte (Hygrohypnum ochraceum). We expressed uptake using the symbol Kd to underscore the relationships between Se in water and Se in plants as “partitioning coefficients” related to the bases of aquatic food chains. A 2-way analysis of variance (ANOVA) was performed with Kd as the dependent variable and season and stream segment (location) as main effects. Selenium concentrations, measured as dissolved Se, total Se, and pore water Se, were also examined. There were significant differences in Kd values with respect to stream segment (P < 0.001); however, the differences were mainly not associated with season, although pore water Se showed a slight association with season (P = 0.052). The interaction effects between season and stream segment were significant for dissolved Se (P = 0.016) and total Se (P = 0.041). Further analysis showed strong negative correlations to the 3 Se water concentrations in spring (dissolved Se: r = –0.973, P < 0.001; total Se: r = –0.972, P < 0.001; pore water Se: r = –0.867, P < 0.001). Fall associations of Kd values to the 3 Se water concentrations were considerably weaker. Dissolved Se and total Se both still showed statistically significant positive correlations to Kd in the fall, but total Se did not. Based on the results of recent studies, it appears that the bryophytes might have preferentially bioconcentrated selenite over selenate in the upper watershed basin rather than in the lower basin. To conclude, the bryophytes appeared to be suitable natural receptors of Se at the bases of numerous food chains in a complex watershed by exhibiting differences in Se uptake based on site location, season, and diverse Se water concentrations.
Dynamic utility: the sixth reciprocity mechanism for the evolution of cooperation

Game theory has been extensively applied to elucidate the evolutionary mechanism of cooperative behaviour. Dilemmas in game theory are important elements that disturb the promotion of cooperation. An important question is how to escape from dilemmas. Recently, a dynamic utility function (DUF) that considers an individual's current status (wealth) and that can be applied to game theory was developed. The DUF is different from the famous five reciprocity mechanisms called Nowak's five rules. Under the DUF, cooperation is promoted by poor players in the chicken game, with no changes in the prisoner's dilemma and stag-hunt games. In this paper, by comparing the strengths of the two dilemmas, we show that the DUF is a novel reciprocity mechanism (sixth rule) that differs from Nowak's five rules. We also show the difference in dilemma relaxation between dynamic game theory and (traditional) static game theory when the DUF and one of the five rules are combined. Our results indicate that poor players unequivocally promote cooperation in any dynamic game. Unlike conventional rules that have to be brought into game settings, this sixth rule is universally (canonical form) applicable to any game because all repeated/evolutionary games are dynamic in principle.