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opencc-zeroApr 2020View details →

Data from: Photonic hybrid state entanglement swapping using cat state superpositions

We propose the use of hybrid entanglement in an entanglement swapping protocol, as means of distributing a Bell state with high fidelity to two parties, Alice and Bob. The hybrid entanglement used in this work is described as a discrete variable (Fock state) and a continuous variable (cat state superposition) entangled state. We model equal and unequal levels of photonic loss between the two propagating continuous variable modes, before detecting these states via a projective vacuum-one-photon measurement, and the other mode via balanced homodyne detection. We investigate homodyne measurement imperfections, and the associated success probability of the measurement schemes chosen in this protocol. We show that our entanglement swapping scheme is resilient to low levels of photonic losses, as well as low levels of averaged unequal losses between the two propagating modes, and show an improvement in this loss resilience over other hybrid entanglement schemes using coherent state superpositions as the propagating modes. Finally, we conclude that our protocol is suitable for potential quantum networking applications which require two nodes to share entanglement separated over a distance of 5-10 km when used with a suitable entanglement purification scheme.

opencc-zeroDec 2016View details →

Data from: Patterns of divergence across the geographic and genomic landscape of a butterfly hybrid zone associated with a climatic gradient

Hybrid zones are a valuable tool for studying the process of speciation and for identifying the genomic regions undergoing divergence and the ecological (extrinsic) and non-ecological (intrinsic) factors involved. Here, we explored the genomic and geographic landscape of divergence in a hybrid zone between Papilio glaucus and Papilio canadensis. Using a genome scan of 28,417 ddRAD SNPs, we identified genomic regions under possible selection and examined their distribution in the context of previously identified candidate genes for ecological adaptations. We showed that differentiation was genome-wide, including multiple candidate genes for ecological adaptations, particularly those involved in seasonal adaptation and host plant detoxification. The Z-chromosome and four autosomes showed a disproportionate amount of differentiation, suggesting genes on these chromosomes play a potential role in reproductive isolation. Cline analyses of significantly differentiated genomic SNPs, and of species diagnostic genetic markers, showed a high degree of geographic coincidence (81%) and concordance (80%) and were associated with the geographic distribution of a climate-mediated developmental threshold (length of the growing season). A relatively large proportion (1.3%) of the outliers for divergent selection were not associated with candidate genes for ecological adaptations and may reflect the presence of previously unrecognized intrinsic barriers between these species. These results suggest that exogenous (climate-mediated) and endogenous (unknown) clines may have become coupled and act together to reinforce reproductive isolation. This approach of assessing divergence across both the genomic and geographic landscape can provide insight about the interplay between the genetic architecture of reproductive isolation and endogenous and exogenous selection.

opencc-zeroFeb 2020View details →

Stable species boundaries despite ten million years of hybridization in tropical eels

Genomic evidence is increasingly underpinning that hybridization between taxa is commonplace, challenging our views on the mechanisms that maintain their boundaries. Here, we focus on seven catadromous eel species (genus Anguilla), and use genome-wide sequence data from more than 450 individuals sampled across the tropical Indo-Pacific, morphological information, and three newly assembled draft genomes to compare contemporary patterns of hybridization with signatures of past gene flow across a time-calibrated phylogeny. We show that the seven species have remained distinct entities for up to 10 million years, despite a dynamic scenario of incomplete isolation whereby the current frequencies of hybridization across species pairs (over 5% of all individuals were either F1 hybrids or backcrosses) contrast remarkably with patterns of past introgression. Based on near-complete asymmetry in the directionality of hybridization and decreasing frequencies of later-generation hybrids, we identify cytonuclear incompatibilities and hybrid breakdown as two powerful mechanisms that can support species cohesion even when hybridization has been pervasive throughout the evolutionary history of entire clades.

opencc-zeroDec 2017View details →

Data from: Mapping reduced introgression loci to the X chromosome of the hybridizing field crickets, Gryllus firmus and G. pennsylvanicus

The genomic architecture of barriers to gene exchange during the speciation process is poorly understood. The genomic islands model suggests that loci associated with barriers to gene exchange prevent introgression of nearby genomic regions via linkage disequilibrium. But few analyses of the actual genomic location of non-introgressing loci in closely related species exist. In a previous study Maroja et al. showed that in the hybridizing field crickets, Gryllus firmus and G. pennsylvanicus, 50 non-introgressing loci are localized on two autosomal regions and the X chromosome, but they were not able to map the loci along the X chromosome because they used a male informative cross. Here, we localize the introgressing and non-introgressing loci on the X chromosome and reveal that all X-linked non-introgressing loci are restricted to a 50-cM region with 10 of these loci mapped to a single location. We discuss the implications of this finding to speciation.

opencc-zeroDec 2018View details →

Assortative mating in hybrid zones is remarkably ineffective in promoting speciation

Partial prezygotic isolation is often viewed as more important than partial postzygotic isolation (low fitness of hybrids) early in the process of speciation. I simulate secondary contact between two populations ('species') to examine effects of assortative mating and low hybrid fitness in preventing blending. A small reduction in hybrid fitness (e.g., by 10%) produces a narrower hybrid zone than a strong but imperfect mating preference (e.g., 10x stronger preference for conspecific over heterospecific mates). In the latter case, rare F1 hybrids find each other attractive (due to assortative mating), leading to the buildup of a continuum of intermediates. The weakness of assortative mating compared to reduced fitness of hybrids in preventing blending is robust to varying genetic bases of these traits. Assortative mating is most powerful in limiting blending when it is encoded by a single locus, is essentially complete, or when there is a large mate search cost. In these cases assortative mating is likely to cause hybrids to have low fitness, due to frequency-dependent mating disadvantage of individuals of rare mating types. These results prompt a questioning of the concept of partial prezygotic isolation, since it is not very isolating unless there is also postzygotic isolation.

opencc-zeroSep 2019View details →

Data from: Preparation and structure of SiOCN fibers derived from cyclic silazane/PAA hybrid precursor

Ceramic matrix composite (CMC) materials have been considered a desired solution for lightweight and high temperature applications. Simultaneously, among all different CMC reinforcements, Polymer-Derived Ceramic (PDC) fibers have gained attention for the intrinsic thermal stability and mechanical strength with simple and cost-effective synthesis techniques. Here, carbon-rich silicon oxycarbide (SiOC) fibers were synthesized via hand-drawing and polymer pyrolysis of a hybrid precursor of 1,3,5,7-tetramethyl-1,3,5,7-tetravinyl-cyclotetrasilazane (TTCSZ) and polyacrylic acid (PAA). The type of silazane reported in this work is considered as a major precursor for SiCN, however it is unspinnable, due to its unfavorable physical properties (low viscosity) and chemical structure (cyclic rather than linear structure). The introduction of PAA to TTCSZ to create a hybrid precursor remarkably improved spinnability of the silazane and should be widely applicable to other unspinnable PDC preceramic polymers. Investigations on structural and compositional development of the fibers were mainly conducted via Raman spectroscopy, Fourier-Transform InfraRed spectroscopy (FTIR), Scanning Electron Microscopy (SEM), X-ray Photoelectron Spectroscopy (XPS), Nuclear Magnetic Resonance (NMR) and ThermoGravimetric Analysis (TGA) to determine spinnability, free carbon content, cross-linking and pyrolysis behavior of the fibers, respectively.

opencc-zeroSep 2015View details →

Lapedo: Hybrid Skeletons for Programming Heterogeneous Multicore Machines in Erlang

We describe Lapedo, a novel library of hybrid parallel skeletons for programming heterogeneous multi-core/many-core CPU/GPU sys- tems in Erlang. Lapedo’s hybrid skeletons comprise a mixture of CPU and GPU components, allowing skeletons to be flexibly and dynamically mapped to available resources. We also describe a model for deriving near-optimal division of work between CPUs and GPUs, ensuring load balancing between resources. Finally, we evaluate the effectiveness of Lapedo on three realistic use cases from different domains, demonstrat- ing significant speedups compared to executing the same application on only CPU cores or a GPU

opencc-zeroAug 2016View details →

Semi-Supervised Active Learning for Sound Classification in Hybrid Learning Environments

There are 16,930 sound instances in our database with durations ranging 242 from 1 to 10 seconds, which correspond to (approximately) 15 hours of environmental 243 sounds. All sound files were converted into raw 16 bit encoding, mono-channel, and 16 244 kHz sampling rate, as various formats and rates were used in the original versions 245 retrieved from the web.

opencc-by-4.0Aug 2016View details →

Semi-Supervised Active Learning for Sound Classification in Hybrid Learning Environments

opencc-by-4.0Jun 2017View details →

A Hybrid Focus Group for the Evaluation of Digital Scholarly Editions of Literary Authors

Data from focus group conducted for DiXiT - Digital Scholarly Editions Initial Training Network. We are studying the use of digital scholarly editions, by observing what users do in interaction with different editions. For this analysis, we chose three digital scholarly editions, designed tasks specific to these editions, confronted typical users with these tasks, and analysed the quality of use in relation to efficiency and effectiveness. The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme FP7/2007-2013/ under REA grant agreement n° 317436.

Data from: Hunting behavior and feeding ecology of Mojave Rattlesnakes (Crotalus scutulatus), Prairie Rattlesnakes (C. viridis), and their hybrids in southwestern New Mexico

Predators must contend with numerous challenges to successfully find and subjugate prey. Complex traits related to hunting are partially controlled by a large number of co-evolved genes which may be disrupted in hybrids. Accordingly, research on the feeding ecology of animals in hybrid zones has shown that hybrids sometimes exhibit transgressive or novel behaviors, yet for many taxa empirical studies of predation and diet across hybrid zones is lacking. We undertook the first such field study for a hybrid zone between two snake species, the Mojave Rattlesnake (Crotalus scutulatus) and Prairie Rattlesnake (C. viridis). Specifically, we leveraged established field methods to quantify hunting behaviors of animals, their prey communities, and diet of individuals across the hybrid zone in southwestern New Mexico, USA. We found that, even though hybrids had significantly lower body condition indices than snakes from either parental lineage, hybrids were generally similar to non-hybrids in hunting behavior, prey encounter rates, and predatory attack and success. We also found that, compared to C. scutulatus, C. viridis was significantly more active while hunting at night and abandoned ambush sites earlier in the morning, and hybrids tended to be more viridis-like in this respect. Prey availability was similar across the study sites, including within the hybrid zone, with Kangaroo Rats (Dipodomys spp.) as the most common small mammal both in habitat surveys and frequency of encounters with hunting rattlesnakes. Analysis of prey remains in stomachs and feces also showed broad similarity in diets, with all snakes preying primarily on small mammals and secondarily on lizards. Taken together, our results suggest that the significantly lower body condition of hybrids does not appear to be driven by differences in their hunting behavior or diet, and may instead relate to metabolic efficiency or other physiological traits we have not yet identified.

Data from: Hybridization and its impact on the ontogenetic allometry of skulls in macaques

The importance of hybridization in morphological diversification is a fundamental topic in evolutionary biology. However, despite accumulated knowledge concerning adult hybrid variations, how hybridization affects ontogenetic allometry is less well understood. Herein, we assessed the effects of hybridization on the postnatal ontogenetic allometry in skulls of a putative hybrid population of introduced Taiwanese macaques (Macaca cyclopis) and native Japanese macaques (M. fuscata). Genomic analyses indicated that the population consisted of individuals with various degrees of admixture, formed by male migration of Japanese to Taiwanese macaques. No marked ontogenetic trajectory angle dissociation was observed in the overall skull shape of hybrids. Transgressive variations in the overall skull shape were observed mainly in non-allometric components. Hybridization collapsed an unknown mechanism found in Japanese macaques that restricts the growth rate of the maxillary sinus (the hollow space in the face), producing hybrids with a mosaic pattern, i.e., the maxillary sinus is as large as that in Taiwanese macaques, although the overall skull shape is intermediate. Our findings suggest that the transgressive variations can be caused by prenatal shape modifications and the lifting of the genetic restriction on the regional growth rate, highlighting the complex genetic and ontogenetic bases underlying hybridization-induced morphological diversification.

Data from: Hybridization and adaptive introgression in a marine invasive species in native habitats

Hybridization of distinct populations or species is an important evolutionary driving force. For invasive species, hybridization can enhance their competitive advantage in the non-native range as a source of adaptive novelty by introgression of selectively favoured alleles. We use single-nucleotide polymorphism arrays (SNP-chips) to assess genetic diversity and population structure in the invasive ctenophore Mnemiopsis leidyi in native habitats along the USA east coast. Hybrids are present at the distribution border of the two lineages. However, our data suggests selection against hybrids in stable habitats, while hybrids are selected for in fluctuating environments. Hybrid populations thriving in extreme and unstable environments of the native range, such as the Chesapeake Bay, could accelerate the invasion success if translocated. For M. leidyi, this is especially relevant as low salinity currently limits its invasion range in western Eurasia. Hybridization status is thus important but currently disregarded to determine high-risk areas for ballast water exchange.

Hybrid dynamic model for shape memory alloy linear and unimorph actuators

Shape memory alloy morphing actuators are a type of soft actuator with many attractive properties. These actuators exhibit large deformation, small form factor, self-sense ability, and physical reservoir computing potential, while also being inexpensive. These morphing actuators are composed of active shape memory alloy wires and a passive base layer that is used to magnify the overall deflection. Although morphing actuators have great potential, the modeling of shape memory alloy actuators is difficult due to both shape memory alloy characteristics and the nonlinearity of the passive layer. Here, a hybrid dynamical model is proposed that couples the phase kinetics & thermal modeling for the shape memory alloy with a dynamic Cosserat nonlinear beam model. This hybrid model is benchmarked against linear and morphing experimental actuators. The model resulted in a root mean squared error of 1.48 mm and 1.63 mm for the morphing actuator configuration for two different actuators. This model can expand the capability and design of novel morphing actuators for a designed deformation profile for use in soft robotics.

Characterizing a lethal mitonuclear incompatibility in naturally hybridizing Xiphophorus swordtails

The evolution of reproductive barriers is the first step in the formation of new species and can help us understand the diversification of life on Earth. These reproductive barriers often take the form of "hybrid incompatibilities," where alleles derived from two different species no longer interact properly in hybrids. Theory predicts that hybrid incompatibilities may be more likely to arise at rapidly evolving genes and that incompatibilities involving multiple genes should be common, but there has been sparse empirical data to evaluate these predictions. Here, we describe a mitonuclear incompatibility involving three genes in physical contact within respiratory Complex I of naturally hybridizing swordtail fish species. Individuals homozygous for mismatched protein combinations fail to complete embryonic development or die as juveniles, while those heterozygous for the incompatibility have reduced Complex I function and unbalanced representation of parental alleles in the mitochondrial proteome. We find that the impacts of different genetic interactions on survival are non-additive, highlighting subtle complexity in the genetic architecture of hybrid incompatibilities. Finally, we document the evolutionary history of the genes involved, showing signals of accelerated evolution and the first case of an incompatibility transferred between species via hybridization.

Data for: Tracking hybrid viability across life-stages in a natural avian contact zone

Hybrid inviability is an important post-zygotic reproductive barrier between species, but emerging signs of reduced viability can be difficult to study across the lifespan of natural hybrids. We use a combination of long-term monitoring, extra-pair paternity and mitochondrial DNA identification in a natural hybrid zone of Ficedula flycatchers to detect emerging signs of intrinsic hybrid inviability across their entire lifespan. We evaluate possible evidence of Darwin's corollary to Haldane's rule, predicting asymmetries in inviability between hybrids resulting from reciprocal crosses, due to incompatible genetic factors with sex-specific inheritance patterns. We found higher hatching failure among mixed-species pairs, possibly indicating early developmental impairments associated with specific parental genetic combinations. Adult hybrids had a higher basal mortality rate than both parental species, and different age-specific mortality trajectories. There were signs of differences in age-independent mortality rates between the reciprocal hybrid crosses: hybrids with a pied flycatcher mother experienced slightly increased mortality later in life. Using an exceptional dataset with many natural hybrids tracked across life stages, we provide evidence for several emerging signs of reduced hybrid viability. Incompatibilities between alleles located on autosomes and uniparentally inherited factors such Z-linked and/or mitochondrial genes are strong candidates underlying intrinsic hybrid dysfunction in this system.

opencc-by-4.0Dec 2023View details →

Subseasonal to Seasonal (S2S) Prediction Algorithms using Hybrid Machine Learning Techniques

< S2S dataset.zip >1.ECMWF observations/hindcast realizations<ul><li>hindcast-like-observations_2000-2019_biweekly_deterministic.zarr</li><li>forecast-like-observations_2020_biweekly_deterministic.zarr</li><li>ecmwf_hindcast-input_2000-2019_biweekly_deterministic.zarr</li><li>ecmwf_forecast-input_2020_biweekly_deterministic.zarr</li><li>hindcast-like-observations_2000-2019_biweekly_tercile-edges.nc</li></ul>2. External variables<ul><li>"nino" folder -> nino12.long.anom.data, nino34.long.anom.data : El Niño data</li><li>"Oscillation" folder<ul><li>-> ersst.v5.pdo.dat.text : PDO (Pacific Decadal Oscillation)</li><li>-> norm.nao.monthly.b5001.current.ascii.table.txt : NAO (North Atlantic Oscillation)</li><li>-> qbo.dat : QBO (Quasi Biennial Oscillation)</li></ul></li><li>"great_lake" folder -> N_seaice_extent_daily_v3.0 : Great lakes ice cover</li><li>observed-solar-cycle-indices.json : Sunspot cycles (two variables: original value and smoothed value)</li></ul>3. Region.txt : Region and its bound4. Biweekly historical statistics data<ul><li>biw_stat_w34 folder -> data (mean, standard deviation, median, skewness, kurtosis) for Week 3-4</li><li>biw_stat_w56 folder -> data (mean, standard deviation, median, skewness, kurtosis) for Week 5-6</li></ul> < ML_code.zip ><ul><li>ML codes for training, testing, and calculating RPSS based on Python3</li><li>Check run_val.sh and run_2020.sh </li></ul>

opencc-zeroDec 2023View details →

Evaluation of tracking performance and robustness for a hybrid locomotion controller

Legged locomotion is a complex control problem that requires both accuracy and robustness to cope with real-world challenges. Legged systems have traditionally been controlled using trajectory optimization with inverse dynamics. Such hierarchical model-based methods are appealing due to intuitive cost function tuning, accurate planning, generalization, and most importantly, the insightful understanding gained from more than one decade of extensive research. However, model mismatch and violation of assumptions are common sources of faulty operation. Simulation-based reinforcement learning, on the other hand, results in locomotion policies with unprecedented robustness and recovery skills. Yet, all learning algorithms struggle with sparse rewards emerging from environments where valid footholds are rare, such as gaps or stepping stones. In this work, we propose a hybrid control architecture that combines the advantages of both worlds to simultaneously achieve greater robustness, foot-placement accuracy, and terrain generalization. Our approach utilizes a model-based planner to roll out a reference motion during training. A deep neural network policy is trained in simulation, aiming to track the optimized footholds. We evaluate the accuracy of our locomotion pipeline on sparse terrains, where pure data-driven methods are prone to fail. Furthermore, we demonstrate superior robustness in the presence of slippery or deformable ground when compared to model-based counterparts. Finally, we show that our proposed tracking controller generalizes across different trajectory optimization methods not seen during training. In conclusion, our work unites the predictive capabilities and optimality guarantees of online planning with the inherent robustness attributed to offline learning.

opencc-zeroDec 2023View details →

Strong plastic responses in aerenchyma formation in F1 hybrids of Imperata cylindrica under different soil moisture conditions

There is insufficient evidence demonstrating how phenotypic plasticity in specific traits mediates hybrid performance. Two ecotypes of Imperata cylindrica produce F1 hybrids. The early flowering type (E-type) in wet habitats has larger internal gas spaces (aerenchyma) than the common type (C-type) in dry habitats. This study evaluated the relationships between the habitat utilisation, aerenchyma plasticity, and growth of I. cylindrica accessions. We hypothesize that plasticity in expressing parental traits explains hybrid establishment in habitats with various soil moisture conditions. Aerenchyma formation was examined in the leaf midribs, rhizomes, and roots of two parental ecotypes and their F1 hybrids in their natural habitats. In common garden experiments, we examined plastic aerenchyma formation in the leaf midribs, rhizomes and roots of natural and artificial F1 hybrids and parental ecotypes. Their vegetative growth performance was also quantified. In the natural habitats where soil moisture content varied widely, the F1 hybrids showed larger variation of aerenchyma formation in the rhizomes than their parental ecotypes. In the common garden experiments, the F1 hybrids showed high plasticity of aerenchyma formation in the rhizomes, and their growth was similar to that of C-type and E-type under drained and flooded conditions, respectively. The results demonstrate that the F1 hybrids of I. cylindrica exhibit plasticity in aerenchyma development in response to varying local soil moisture content. This characteristic allows the hybrids to thrive in diverse soil moisture conditions.