Separate Expansions Research Articles

ContextAD: Context-Aware Acronym Disambiguation with Siamese BERT Network

Acronym disambiguation is the process of determining the correct expansion of an acronym in given context, which can assist many downstream natural language processing tasks. Typically, existing methods on this task will directly perform semantic comparisons between the candidate expansions and the original sentence, ignoring the relevance of contextual information to expansions. To solve this issue, this paper proposes a context-aware acronym disambiguation method with Siamese BERT network (ContextAD). First, we combine each candidate expansion with corresponding acronym’s context to form a new sentence set. Then, the new and original sentences are input into a Siamese BERT network that can obtain the semantic similarity. The new sentences and the separate candidate expansions are input into the Siamese BERT network, respectively, along with the original sentences, which can obtain another semantic similarity. Finally, the two different semantic similarities are combined to determine the most suitable expansion. We quantify the improvement of our proposed ContextAD model against a state-of-the-art baseline using the public dataset of the shared tasks of acronym disambiguation (AD) held under AAAI-2021 workshop on SDU and show that it achieves a better performance based on the same BERT model.

Design of the shattered pellet injection system for ASDEX Upgrade

A new shattered pellet injection system was designed and built to perform disruption mitigation experiments on ASDEX Upgrade. The system can inject pellets with diameters of 1, 2, 4, or 8 mm with variable lengths over a range of L/D ratios of ∼0.5–1.5. By using helium or deuterium as propellant gas, the pellets can be accelerated to speeds between 60 and 750 m/s. The velocity range slightly depends on the pellet mass. The injection system is capable of preparing three pellets in separate barrels at the same time. Once accelerated by the propellant gas pulse, the pellets travel through one of three parallel flight tubes. Each flight tube is separated into three sections with increasing diameters of 12, 14, and 16 mm. Two gaps between the sections allow for removal of the propellant gas by expansion into two separate expansions tanks (0.3 and 0.035 m3), pellet observation in the first gap and the torus gate valve in the second. Each flight tube end is equipped with an exchangeable shatter head with different shatter angles, square or circular cross-section, and different lengths. The gas preparation and control systems allow highly automated pellet generation for precision of the pellet composition and an excellent reproducibility of shattered pellet experiments.

The gold-ringed octopus (Amphioctopus fangsiao) genome and cerebral single-nucleus transcriptomes provide insights into the evolution of karyotype and neural novelties

BackgroundColeoid cephalopods have distinctive neural and morphological characteristics compared to other invertebrates. Early studies reported massive genomic rearrangements occurred before the split of octopus and squid lineages (Proc Natl Acad Sci U S A 116:3030-5, 2019), which might be related to the neural innovations of their brain, yet the details remain elusive. Here we combine genomic and single-nucleus transcriptome analyses to investigate the octopod chromosome evolution and cerebral characteristics.ResultsWe present a chromosome-level genome assembly of a gold-ringed octopus, Amphioctopus fangsiao, and a single-nucleus transcriptome of its supra-esophageal brain. Chromosome-level synteny analyses estimate that the chromosomes of the ancestral octopods experienced multiple chromosome fission/fusion and loss/gain events by comparing with the nautilus genome as outgroup, and that a conserved genome organization was detected during the evolutionary process from the last common octopod ancestor to their descendants. Besides, protocadherin, GPCR, and C2H2 ZNF genes are thought to be highly related to the neural innovations in cephalopods (Nature 524:220–4, 2015), and the chromosome analyses pinpointed several collinear modes of these genes on the octopod chromosomes, such as the collinearity between PCDH and C2H2 ZNF, as well as between GPCR and C2H2 ZNF. Phylogenetic analyses show that the expansion of the octopod protocadherin genes is driven by a tandem-duplication mechanism on one single chromosome, including two separate expansions at 65 million years ago (Ma) and 8–14 Ma, respectively. Furthermore, we identify eight cell types (i.e., cholinergic and glutamatergic neurons) in the supra-esophageal brain of A. fangsiao, and the single-cell expression analyses reveal the co-expression of protocadherin and GPCR in specific neural cells, which may contribute to the neural development and signal transductions in the octopod brain.ConclusionsThe octopod genome analyses reveal the dynamic evolutionary history of octopod chromosomes and neural-related gene families. The single-nucleus transcriptomes of the supra-esophageal brain indicate their cellular heterogeneities and functional interactions with other tissues (i.e., gill), which provides a foundation for further octopod cerebral studies.

Draft genome of six Cuban Anolis lizards and insights into genetic changes during their diversification

BackgroundDetecting genomic variants and their accumulation processes during species diversification and adaptive radiation is important for understanding the molecular and genetic basis of evolution. Anolis lizards in the West Indies are good models for studying evolutionary mechanisms because of the repeated evolution of their morphology and the ecology. We performed de novo genome assembly of six Cuban Anolis lizards with different ecomorphs and thermal habitats (Anolis isolepis, Anolis allisoni, Anolis porcatus, Anolis allogus, Anolis homolechis, and Anolis sagrei). We carried out a comparative analysis of these genome assemblies to investigate the genetic changes that occurred during their diversification.ResultsWe reconstructed novel draft genomes with relatively long scaffolds and high gene completeness, with the scaffold N50 ranging from 5.56 to 39.79 Mb and vertebrate Benchmarking Universal Single-Copy Orthologs completeness ranging from 77.5% to 86.9%. Comparing the repeat element compositions and landscapes revealed differences in the accumulation process between Cuban trunk-crown and trunk-ground species and separate expansions of several families of LINE in each Cuban trunk-ground species. Duplicated gene analysis suggested that the proportional differences in duplicated gene numbers among Cuban Anolis lizards may be associated with differences in their habitat ranges. Additionally, Pairwise Sequentially Markovian Coalescent analysis suggested that the effective population sizes of each species may have been affected by Cuba’s geohistory.ConclusionsWe provide draft genomes of six Cuban Anolis lizards and detected species and lineage-specific transposon accumulation and gene copy number changes that may be involved in adaptive evolution. The change processes in the past effective population size was also estimated, and the factors involved were inferred. These results provide new insights into the genetic basis of Anolis lizard diversification and are expected to serve as a stepping stone for the further elucidation of their diversification mechanisms.

Maize dispersal patterns associated with different types of endosperm and migration of indigenous groups in lowland South America.

The lowlands of South America appear to be remarkably important in the evolutionary history of maize, due to new evidence that suggests that maize dispersed from Mexico and arrived in this region in a state of partial domestication. This study aimed to identify dispersal patterns of maize genetic diversity in this part of the continent. A total of 170 maize accessions were characterized with 4398 single nucleotide polymorphisms (SNPs) and analysed to determine if maize dispersal was associated with types of endosperm and indigenous language families. Four genetic groups were identified in the discriminant analysis of principal components and five groups in the cluster analysis (neighbour-joining method). The groups were structured according to the predominance of endosperm types (popcorn, floury, flint/semi-flint). Spatial principal component analysis of genetic variation suggests different dispersal patterns for each endosperm type and can be associated with hypotheses of expansions of different indigenous groups. From a possible origin in Southwestern Amazonia, different maize dispersal routes emerged: (1) towards Northern Amazonia, which continued towards the Caatinga and south-eastern Atlantic Forest (Floury); (2) towards Southern Brazil, passing through the Cerrado and Southern Atlantic Forest reaching the Pampa region (Floury); and (3) along the Atlantic Coast, following Tupi movements originating from two separate expansions: one (Tupinamba) from north to south, and the other (Guarani) in the opposite direction, from south to north (flint, floury and popcorn).

Bianchi type-I cosmological model with Tsallis holographic dark energy in f(R,T) theory of gravity

Objectives: In the f(R, T) theory of gravity, to examine the Bianchi type-I model with dark matter and Tsallis holographic dark energy (THDE). Method: To acquire exact solutions of the field equations, we used THDE density and two separate volumetric expansions. The model’s physical properties are compared to current observational evidence. Findings/ Novelty: The universe is in accelerating stage for both volumetric expansion models and it reaches isotropy at a delayed time, according to the study of the deceleration parameter. In addition, our model acts as a lambda model. Keywords: Bianchi type-I; THDE; f(R T) gravity; Isotropy; Lambda model

On the spatially asymptotic structure of time-periodic solutions to the Navier–Stokes equations

The asymptotic behavior of weak time-periodic solutions to the Navier–Stokes equations with a drift term in the three-dimensional whole space is investigated. The velocity field is decomposed into a time-independent and a remaining part, and separate asymptotic expansions are derived for both parts and their gradients. One observes that the behavior at spatial infinity is determined by the corresponding Oseen fundamental solutions.

When parasites persist: tapeworms survive host extinction and reveal waves of dispersal across Beringia.

Investigations of intercontinental dispersal between Asia and North America reveal complex patterns of geographic expansion, retraction and isolation, yet historical reconstructions are largely limited by the depth of the record that is retained in patterns of extant diversity. Parasites offer a tool for recovering deep historical insights about the biosphere, improving the resolution of past community-level interactions. We explored biogeographic hypotheses regarding the history of dispersal across Beringia, the region intermittently linking Asia and North America, through large-scale multi-locus phylogenetic analyses of the genus Schizorchis, an assemblage of host-specific cestodes in pikas (Lagomorpha: Ochotonidae). Our genetic data support palaeontological evidence for two separate geographic expansions into North America by Ochotona in the late Tertiary, a history that genomic evidence from extant pikas does not record. Pikas descending from the first colonization of Miocene age persisted into the Pliocene, subsequently coming into contact with a second wave of Nearctic colonists from Eurasia before going extinct. Spatial and temporal overlap of historically independent pika populations provided a window for host colonization, allowing persistence of an early parasite lineage in the contemporary fauna following the extinction of its ancestral hosts. Empirical evidence for ancient 'ghost assemblages' of hosts and parasites demonstrates how complex mosaic faunas are assembled in the biosphere through episodes of faunal mixing encompassing parasite lineages across deep and shallow time.

Plastid phylogenomic insights into the evolution of subfamily Dialioideae (Leguminosae)

The subfamily Dialioideae (Leguminosae) consists of 17 genera and about 85 species. Previous studies have detected significant plastid genome (plastome) structure variations in legumes, particularly in subfamilies Papilionoideae and Caesalpinioideae. Hence it is important to investigate plastomes from the newly recognized Dialioideae to better understand the plastome variation across the whole family. Here, we used nine plastomes representing nine genera of Dialioideae to explore plastome structural variation and intergeneric relationships in this subfamily. All plastomes of Dialioideae exhibited a typical quadripartite structure, and had relatively conserved structure compared with other legume subfamilies. However, the genome size ranged from 154,124 bp to 165,973 bp and gene numbers ranged from 129 to 132, mainly due to the expansion and contraction of the inverted repeat (IR) regions. The IR of Distemonanthusbenthamianus has experienced two separate expansions into the large single copy (LSC) region and the small single copy (SSC) region, and one contraction from SSC. Poeppigiaprocera has experienced two separate IR expansions into LSC, while Dicoryniaparaensis has experienced an IR contraction from LSC. Highly divergent regions or genes (ndhC−trnVUAC,psbK−trnQUUG,rps19−rps3,rpl33−rps18,accD−psaI,trnGUCC−trnSGCU,psbI−trnSGCU,5′rps16−trnQUUG and ycf1) were identified as potential molecular markers for further species delimitation and population genetics analysis in legumes. Phylogenetic analysis based on 77 protein-coding sequences fully resolved the intergeneric relationships among nine genera except a moderately supported sister relationship between Petalostylislabicheoides and Labichealanceolata. Our study reveals new insights into the structural variations of plastomes in subfamily Dialioideae and advances our understanding of the evolutionary trajectories of legume plastomes.

Staggering Effects in Nuclear and Molecular Spectra

It is shown that the recently observed AI = 2 staggering seen in superdeformed nuclear bands is also occurring in certain electronically excited rotational bands of diatomic molecules, in which it is attributed to interband interactions (bandcrossings). In addition, a AI = 1 staggering effect (i.e. a relative displacement of the levels with even angular momentum I with respect to the levels of the same band with odd /) is seen in molecular bands free from AI = 2 staggering (i.e. free from interband interactions/bandcrossings). The magnitude of the AI = 1 staggering is found to be constant as a function of 7, in agreement with the predictions of algebraic models (u(ll) model, u(16) model, Vector Boson Model) used for the description of octupole nuclear bands, i.e. bands corresponding to pear-like shapes, suggesting that the presence of AI = 1 staggering in rotational bands of diatomic molecules could be attributed in general to the inequality of the masses of the two atoms of which the molecule is composed. The existence of the AI = 1 staggering effect is corroborated by the fact that separate Dunham expansions for the even levels and the odd levels of such bands give similar but different parameter sets.

A crank-kinematics-based engine cylinder pressure reconstruction model

A new inverse model is proposed for reconstructing steady-state and transient engine cylinder pressure using measured crank kinematics. An adaptive nonlinear time-dependent relationship is assumed between windowed-subsections of cylinder pressure and measured crank kinematics in a time-domain format (rather than in crank-angle domain). This relationship comprises a linear sum of four separate nonlinear functions of crank jerk, acceleration, velocity and crank angle. Each of these four nonlinear functions is obtained at each time instant by fitting separate m-term Chebyshev polynomial expansions, where the total 4 m instantaneous expansion coefficients are found using a standard (overdetermined) linear least-square solution method. A convergence check on the calibration accuracy shows that this initially improves as more Chebyshev polynomial terms are used, but with further increase, the overdetermined system becomes singular. Optimal accuracy Chebyshev expansions are found to be of degree m = 4, using 90 or more cycles of engine data to fit the model. To confirm the model accuracy in predictive mode, a defined measure is used, namely the ‘ calibration peak pressure error’. This measure allows effective a priori exclusion of occasionally unacceptable predictions. The method is tested using varying speed data taken from a three-cylinder direct-injection spark ignition engine fitted with cylinder pressure sensors and a high-resolution shaft encoder. Using appropriately filtered crank kinematics (plus the ‘calibration peak pressure error’), the model produces fast and accurate predictions for previously unseen data. Peak pressure predictions are consistently within 6.5% of target, whereas locations of peak pressure are consistently within ±2.7 °CA. The computational efficiency makes it very suitable for real-time implementation.

Viscoplastic fluids in 2D plane squeeze flow: A matched asymptotics analysis

A matched asymptotic expansions approach is used to determine the flow behaviour of Casson and Herschel–Bulkley fluids between two parallel plates that are approaching each other with a constant velocity. The present study is based on the earlier work of Muravleva (2015), who has analyzed the squeeze flow of a Bingham fluid using the method of matched asymptotic expansions. A naive application of classical lubrication theory leads to a kinematic inconsistency in the predicted plug region - the well known “squeeze flow paradox” for a viscoplastic fluid. The objective of this work is to determine a consistent solution for the aforementioned constitutive equations. Based on the technique of matched asymptotic expansions, the solution is formulated in terms of separate expansions in the regions adjacent to the two plates where the shear stress is dominant, and a central pseudo-plug (plastic) region where the normal stresses become comparable to the shear stress; the two regions being separated by a pseudo-yield surface. In this manner, a complete asymptotic solution is developed for the squeeze flow of both Casson and Herschel–Bulkley fluid models. Using this solution, we derive expressions for the velocity, pressure and stress fields, and the squeeze force acting to retard the plates. The effect of the yield threshold on the pseudo-yield surface that separates the sheared and plastic zones, pressure distribution and squeeze force is investigated.

The Multi-PN approximation to neutron transport equation

The Multi-PN (MPN) approximation to the first-order neutron transport equation in one- and two-dimensional geometries is presented using a variational approach. The directional variations of the angular flux have been modeled by separate spherical harmonics expansions in M subdomains, while finite elements have been utilized to represent the spatial dependence. A straightforward procedure has been proposed to handle any order of discretized polynomial expansions in both isotropic and anisotropic scattering medium. A key problem with much of the literature regarding the full-range spherical harmonic method is that it cannot exactly describe the discontinuous nature of the angular flux. Thus, the use of customary expansions leads to substantial defect at boundary and interface of two distinct media (e.g. interface of fuel elements and moderators). The major contribution of the MPN discretization is a theory that overcomes these difficulties. The work represents the generalization of the Double-PN (DPN) approximation previously applied to the neutron transport equation. Numerical results in one- and two-dimensional problems compare MPN and customary PN calculations to the reference transport calculations.

Spatial Intratumor Genomic Heterogeneity within Localized Prostate Cancer Revealed by Single-nucleus Sequencing

BackgroundProstate adenocarcinoma (PCa) is a complex genetic disease, and the implementation of personalized treatment in PCa faces challenges due to significant inter- and intrapatient tumor heterogeneities. ObjectiveTo systematically explore the genomic complexity of tumor cells with different Gleason scores (GSs) in PCa. Design, setting, and participantsWe performed single-cell whole genome sequencing of 17 tumor cells from localized lesions with distinct GS and matched four normal samples from two prostatectomy patients. Outcome measurements and statistical analysisAll classes of genomic alterations were identified, including substitutions, insertions/deletions, copy number alterations, and rearrangements. Results and limitationsSignificant spatial, intra- and intertumoral heterogeneities were observed at the cellular level. In the patient 1, all cells shared the same TP53 driver mutation, implying a monoclonal origin of PCa. In the patient 2, only a subpopulation of cells contained the TP53 driver mutation, whereas other cells carried different driver mutations, indicating a typical polyclonal model with separate clonal cell expansions. The tumor cells from different sides of prostate owned various mutation patterns. Considerable neoantigens were predicted among different cells, implying unknown immune editing components helping prostate tumor cells escaping from immune surveillance. ConclusionsThere is a significant spatial genomic heterogeneity even in the same PCa patient. Our study also provides the first genome-wide evidence at single-cell level, supporting that the origin of PCa could be either polyclonal or monoclonal, which has implications for treatment decisions for prostate cancer. Patient summaryWe reported the first single-cell whole genomic data of prostate adenocarcinoma (PCa) from different Gleason scores. Identification of these genetic alterations may help understand PCa tumor progression and clonal evolution.

Asymptotic Solutions of the Planar Squeeze Flow of a Herschel-Bulkley Fluid

In this study, we present the analysis of the squeeze flow of a Herschel-Bulkley fluid between parallel plates that are approaching each other with a constant squeeze motion. The classical lubrication analysis predicts the existence of a central unyielded zone bracketed between near-wall regions. This leads to the well-known squeeze flow paradox for viscoplastic fluids. Since the kinematic arguments show that there must be a finite velocity gradient even in the unyielded zone, thereby precluding the existence of such regions. This paradox may, however, be resolved within the framework of a matched asymptotic expansions approach where one postulates separate expansions within the yielded and apparently unyielded (plastic) zones. Based on the above technique, we circumvent the paradox, and develop complete asymptotic solutions for the squeeze flow of a Herschel-Bulkley fluid. We derive expressions for the velocity, pressure and squeeze force. The effects of the yield threshold on the pseudo-yield surface that separates the sheared and plastic zones, and squeeze force for different values of non-dimensional yield stress have been investigated.

De Novo Mutations Resolve Disease Transmission Pathways in Clonal Malaria.

Detecting de novo mutations in viral and bacterial pathogens enables researchers to reconstruct detailed networks of disease transmission and is a key technique in genomic epidemiology. However, these techniques have not yet been applied to the malaria parasite, Plasmodium falciparum, in which a larger genome, slower generation times, and a complex life cycle make them difficult to implement. Here, we demonstrate the viability of de novo mutation studies in P. falciparum for the first time. Using a combination of sequencing, library preparation, and genotyping methods that have been optimized for accuracy in low-complexity genomic regions, we have detected de novo mutations that distinguish nominally identical parasites from clonal lineages. Despite its slower evolutionary rate compared with bacterial or viral species, de novo mutation can be detected in P. falciparum across timescales of just 1–2 years and evolutionary rates in low-complexity regions of the genome can be up to twice that detected in the rest of the genome. The increased mutation rate allows the identification of separate clade expansions that cannot be found using previous genomic epidemiology approaches and could be a crucial tool for mapping residual transmission patterns in disease elimination campaigns and reintroduction scenarios.

On asymptotic expansion solvers for highly oscillatory semi-explicit DAEs

The paper is concerned with the discretization and solution of DAEs of index $1$ and subject to a highly oscillatory forcing term. Separate asymptotic expansions in inverse powers of the oscillatory parameter are constructed to approximate the differential and algebraic variables of the DAEs. The series are truncated to enable practical implementation. Numerical experiments are provided to illustrate the effectiveness of the method.

Pleistocene Mitochondrial Genomes Suggest a Single Major Dispersal of Non-Africans and a Late Glacial Population Turnover in Europe

How modern humans dispersed into Eurasia and Australasia, including the number of separate expansions and their timings, is highly debated [1, 2]. Two categories of models are proposed for the dispersal of non-Africans: (1) single dispersal, i.e., a single major diffusion of modern humans across Eurasia and Australasia [3-5]; and (2) multiple dispersal, i.e., additional earlier population expansions that may have contributed to the genetic diversity of some present-day humans outside of Africa [6-9]. Many variants of these models focus largely on Asia and Australasia, neglecting human dispersal into Europe, thus explaining only a subset of the entire colonization process outside of Africa [3-5, 8, 9]. The genetic diversity of the first modern humans who spread into Europe during the Late Pleistocene and the impact of subsequent climatic events on their demography are largely unknown. Here we analyze 55 complete human mitochondrial genomes (mtDNAs) of hunter-gatherers spanning ∼35,000 years of European prehistory. We unexpectedly find mtDNA lineage M in individuals prior to the Last Glacial Maximum (LGM). This lineage is absent in contemporary Europeans, although it is found at high frequency in modern Asians, Australasians, and Native Americans. Dating the most recent common ancestor of each of the modern non-African mtDNA clades reveals their single, late, and rapid dispersal less than 55,000 years ago. Demographic modeling not only indicates an LGM genetic bottleneck, but also provides surprising evidence of a major population turnover in Europe around 14,500 years ago during the Late Glacial, a period of climatic instability at the end of the Pleistocene.

Phylogeography of Eastern Grey Kangaroos, Macropus giganteus, Suggests a Mesic Refugium in Eastern Australia

Phylogeographic studies around the world have identified refugia where fauna were able to persist during unsuitable climatic periods, particularly during times of glaciation. In Australia the effects of Pleistocene climate oscillations on rainforest taxa have been well studied but less is known about the effects on mesic-habitat fauna, such as the eastern grey kangaroo (Macropus giganteus). The eastern grey kangaroo is a large mammal that is common and widespread throughout eastern Australia, preferring dry mesic habitat, rather than rainforest. As pollen evidence suggests that the central-eastern part of Australia (southeast Queensland and northern New South Wales) experienced cycles of expansion in mesic habitat with contraction in rainforests, and vice versa during glacial and interglacial periods, respectively, we hypothesise that the distribution of the eastern grey kangaroo was affected by these climate oscillations and may have contracted to mesic habitat refugia. From 375 mitochondrial DNA control region sequences from across the distribution of eastern grey kangaroos we obtained 108 unique haplotypes. Phylogenetic analysis identified two clades in Queensland, one of which is newly identified and restricted to a small coastal region in southern Queensland north of Brisbane, known as the Sunshine Coast. The relatively limited geographic range of this genetically isolated clade suggests the possibility of a mesic habitat refugium forming during rainforest expansion during wetter climate cycles. Other potential, although less likely, reasons for the genetic isolation of the highly distinct clade include geographic barriers, separate northward expansions, and strong local adaptation.

Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue.

Whole genome DNA sequencing was used to decrypt the phylogeny of multiple samples from distinct areas of cancer and morphologically normal tissue taken from the prostates of three men. Mutations were present at high levels in morphologically normal tissue distant from the cancer reflecting clonal expansions, and the underlying mutational processes at work in morphologically normal tissue were also at work in cancer. Our observations demonstrate the existence of on-going abnormal mutational processes, consistent with field-effects, underlying carcinogenesis. This mechanism gives rise to extensive branching evolution and cancer clone mixing as exemplified by the coexistence of multiple cancer lineages harboring distinct ERG fusions within a single cancer nodule. Subsets of mutations were shared either by morphologically normal and malignant tissue or between different ERG-lineages, indicating earlier or separate clonal cell expansions. Our observations inform on the origin of multifocal disease and have implications for prostate cancer therapy in individual cases.