Character Reconstruction Research Articles

Deep Neural Network Model-Assisted Reconstruction and Optimization of Chinese Characters in Product Packaging Graphic Patterns and Visual Styling Design

Chinese character fonts not only carry the long history of Chinese civilization, but also burst out modern design art elements with distinctive Chinese characteristics. This article first analyzes the origin and writing form of several ancient Chinese characters and draws out the influence of the historical evolution of ancient Chinese characters on Chinese culture. In the basic theoretical structure of font design, traditional art elements and modern font design are integrated, and specific design cases are analyzed. A Chinese character packaging quality detection method combining machine vision and a lightweight convolutional neural network is proposed. First, the method based on threshold segmentation and affine transformation in machine vision is used to perform threshold processing on the image to be tested, and the Chinese character region is tilted and cropped; then, the network structure of the classification algorithm is designed according to the requirements of image features and defect recognition. The field images are produced, a dataset of Chinese character packaging defects is established, and then the proposed Chinese character packaging defect recognition network is verified and deployed to test the accuracy and detection speed of the algorithm deployed on the Jetson Nano embedded platform. Combined with theoretical research and case analysis, the design of packaging design series is practiced with the idea of combining Chinese character art design and classical culture.

О МОДУСАХ ФРАГМЕНТАРНОГО ПИСЬМА (СЕМЬ ФРАГМЕНТОВ)

I offer an ensemble of seven fragments featuring modernist and postmodernist authors who practiced fragmentary writing. Fragmented writing is seen as a way of addressing the epistemological problem of part and whole, the aesthetic architectonics of part and whole, as well as existential issues (death, end / nonfinalism). Accordingly, through the prism of modernist artists (Schwitters, Bellmer, Rilke, Mandelstam), the attitude to fragment and whole is demonstrated, which forms a special poetics of dissociation of speech, reconstruction and deconstruction of artifact body and novel character, subversion of narrative mechanisms, including problematization of visual work frame, beginning and end of narrative text. It is revealed that the destructed, fragmented image of the world is often expressed in traditional genres or exploited by stylizing and parodying them. Wittgenstein, Benjamin, Adorno and Hamacher are considered as philosophers and philologists who have chosen the form of fragment (collection of aphorisms, notes and extracts, quotations). In their modus operandi of reflection and style there is a connection with the early Romantic tradition of the fragment, according to which the fragment is both an isolated, completed short text and part of the whole (in the pragmatic sense, an ensemble of fragments; in the epistemological sense, an absolute whole). For Schlegel and Novalis the connection between the fragment and the whole was thought of as an anticipation of the whole in an infinite series of acts of reflection: the whole is unattainable, but the process is infinite. In the 20th and 21st centuries the difficulty, up to complete negation in poststructuralism, of grasping the transcendental signifier evokes a sense of melancholy and nostalgia, and provokes a utopian return to archaic, ascetic escapism. Fragmented writing thus becomes a form of reaction to the modernist acceleration of time, the instrumentalization of the mind and the alienation of the person. The review presented here is stylized in the form of notes-fragments, linked by leitmotifs and a number of ideas that allow not only the construction but also the problematization of fragmented writing.

Absence of some cytochrome P450 (CYP) and hydroxysteroid dehydrogenase (HSD) enzymes in hagfishes

Corticosteroids are synthesized from cholesterol by steroidogenic enzyme catalysts belonging to two main families: the cytochrome p450s (CYPs) and hydroxysteroid dehydrogenases (HSDs). The action of these steroidogenic enzymes allows the genesis of the terminal active corticosteroids 11-deoxycortisol (S), 1ɑ-hydroxycorticosterone (1α-OH-B), or cortisol in different fish species. However, for Cyclostomes like hagfishes, the terminal corticosteroid is still undefined. In this study, we examined the presence or absence of CYPs and HSDs as traits in fishes to gain insight about the primary corticosteroid synthesis pathways of the hagfishes. We used published cytochrome c oxidase I (COXI) amino acid sequences to construct a phylogeny of fishes and then mapped the CYPs and HSDs as morphological traits onto the tree to predict the ancestral character states through ancestral character reconstruction (ACR). There is a clear phylogenetic signal for CYP (i.e., CYP11a1, 17, 21, and 11b) and HSD (i.e., 11-βHSD and 3β-HSD) derivatives of interest throughout the more derived fishes. Using trait-based ACR, we also found that hagfishes possess genes for 3β-HSD, CYP11a1, CYP17, and CYP21. Importantly, the presence of CYP21 implies that hagfish can synthesize 11-deoxycorticosterone (11-DOC) and S. Previous research demonstrated that despite hagfish having CYP21, neither 11-DOC nor S could be detected in hagfish. This discrepancy between the presence of steroidogenic enzymes and products brings into question the expression and/or function of CYP21 in hagfishes.

Recurrent evolutionary changes in pollen shape and ornamentation of the vataireoid clade (Papilionoideae, Fabaceae), an early-branching lineage of florally divergent genera

Abstract Pollen traits have clarified the classification and understanding of the evolutionary history of different groups of angiosperms, due to their wide morphological diversity. To increase our knowledge on the morphological evolution of the vataireoid clade (Fabaceae, Papilionoideae), a lineage comprising 30 species of Neotropical trees in the genera Luetzelburgia, Sweetia, Vatairea and Vataireopsis, pollen materials of 26 species were acetolysed and analysed using light and scanning electron microscopy. Characters were defined to reconstruct the pollen evolution in each of the ancestral nodes of the phylogenetic tree of the clade using Bayesian stochastic character mapping. All vataireoid genera have relatively variable pollen morphology, ranging from small to medium and subtriangular to circular amb, and their aperture margo may be present or absent. The exine ornamentation varies greatly across the clade: perforate (L. praecox and S. fruticosa); rugulate (L. andradelimae); rugulate-foveolate-perforate (Vatairea guianensis and Vatairea heteroptera); reticulate (Vataireopsis araroba) and microreticulate in most species. Analyses of ancestral character reconstruction revealed multiple events of independent evolution in all pollen traits during the diversification of the vataireoid clade in the last 16 Myr, since the Miocene. Just as evolutionary transitions in floral architecture were so recurrent in the vataireoid clade, pollen evolution was relatively labile and exhibited little phylogenetic conservatism in shape or ornamentation.

Untargeted Metabolomics Sheds Light on the Diversity of Major Classes of Secondary Metabolites in the Malpighiaceae Botanical Family.

Natural products produced by plants are one of the most investigated natural sources, which substantially contributed to the development of the natural products field. Even though these compounds are widely explored, the literature still lacks comprehensive investigations aiming to explore the evolution of secondary metabolites produced by plants, especially if classical methodologies are employed. The development of sensitive hyphenated techniques and computational tools for data processing has enabled the study of large datasets, being valuable assets for chemosystematic studies. Here, we describe a strategy for chemotaxonomic investigations using the Malpighiaceae botanical family as a model. Our workflow was based on MS/MS untargeted metabolomics, spectral searches, and recently described in silico classification tools, which were mapped into the latest molecular phylogeny accepted for this family. The metabolomic analysis revealed that different ionization modes and extraction protocols significantly impacted the chemical profiles, influencing the chemotaxonomic results. Spectral searches within public databases revealed several clades or genera-specific molecular families, being potential chemical markers for these taxa, while the in silico classification tools were able to expand the Malpighiaceae chemical space. The classes putatively annotated were used for ancestral character reconstructions, which recovered several classes of metabolites as homoplasies (i.e., non-exclusive) or synapomorphies (i.e., exclusive) for all sampled clades and genera. Our workflow combines several approaches to perform a comprehensive evolutionary chemical study. We expect it to be used on further chemotaxonomic investigations to expand chemical knowledge and reveal biological insights for compounds classes in different biological groups.

A first phylogenetic hypothesis for the diverse genus Conophytum (Ruschieae, Ruschioideae, Aizoaceae) suggests convergent evolution of floral syndromes

Pollinator specialisation is one of the major drivers of angiosperm diversification in the Greater Cape Floristic Region (GCFR) of South Africa. Conophytum (Aizoaceae) is a flagship genus for the underexplored arid regions of the GCFR (ca. 108 spp.) with 83.9% of its species endemic to this region and has a floral structure that is unique within the rapidly diversified Ruschieae (Aizoaceae). Floral traits, together with leaf characters divide the genus into 16 sections. We present here the first phylogenetic hypothesis for Conophytum, based on molecular data. The combined phylogenetic data for six plastid regions (matK, rpl16, rps16, trnL-F, trnQ-rps16 and trnS-trnG) were analysed using Bayesian inference, maximum likelihood and maximum parsimony to test the evolution of this floral diversity and current sectional classification. Conophytum was recovered as monophyletic including the three small genera Berrisfordia L.Bolus, Herreanthus Schwantes and Ophthalmophyllum Dinter & Schwantes. Six strongly supported clades were recovered within Conophytum: while several of the sections were broadly retrieved within these clades, the more morphologically variable sections such as Minuscula and Wettsteinia were not supported by our data. The distributions of the six clades largely overlap and are generally confined to the arid parts of the GCFR within South Africa, with only one clade extending into the southern wetter parts. Ancestral character reconstructions showed that floral traits evolved multiple times with low phylogenetic signal recovered for autumn- and winter-flowering and flower type, while the other traits indicated no phylogenetic signal. This lack of phylogenetic signal suggests that drivers of diversity in Conophytum are possibly linked to adaptation to pollinators, with a high rate of inferred pollination shifts observed, i.e. 1.7 shifts per species, mirroring that of Lapeirousia (Iridacaeae) in the GCFR. The evolution of unique tubular flowers and shift to autumn-flowering were recovered as traits indicating strong phylogenetic signal and may have enabled Conophytum to exploit a range of pollinators through diversification in floral morphologies.

Morphology, molecular phylogeny and systematics of the diatom genus Fallacia (Sellaphoraceae), with descriptions of three new species1.

Fallacia is distinguished morpho-anatomically from Navicula sensu lato based on the possession of an H-shaped chloroplast, lateral sterna and a finely porous conopeum, but whether this genus is monophyletic is still in question. Three new Fallacia species are described based on morphology and SSU rRNA and rbcL gene sequences: Fallacia tateyamensis sp. nov., Fallacia bosoensis sp. nov. and Fallacia laevis sp. nov. We performed the first comprehensive molecular and morphological phylogenetic analyses of 31 Fallacia species based on 11 new sequences from six species and 23 morphological characters. We also documented the detailed morphogenesis of Fallacia for the first time. Fallacia is not monophyletic. Both morphological and DNA sequence data supported the separation of Rossia from Fallacia, while the phylogenetic position of Pseudofallacia is uncertain. We recognized four morphogroups in Fallacia by morphological and molecular phylogenetic analyses. Ancestral character reconstruction indicated that diatoms in Sellaphoraceae evolved from the possession of two lateral narrow parallel depressions covered by narrow nonporous conopea, to lyre-shaped canals covered by wide porous conopea. Lanceolate canals and the presence of areolae in canals evolved multiple times independently.

Phylogeographical and evolutionary history of variola major virus; a question of timescales?

Aim of this study was to reconstruct the phylogeography of variola virus (VARV) in the XX century, using 47 VARV whole genome sequences available in public databases, through two different methods for ancestral character reconstruction: a frequently used Bayesian framework and a fast maximum-likelihood (ML) based method. The substitution rate of the whole VARV genome was estimated to be between 6.7×10-6 and 1.1×10-5 substitutions/site/year. Both ML and Bayesian methods gave similar trees topology, showing two distinct monophyletic groups: one (known as P1) including the great part of variola major and the second (P2) including West African and American (variola minor) isolates and close evolutionary rate estimations, between 6.73×10-6 and 1.1×10-5 for the whole genome. The phylogeographical reconstruction of P1 suggested that the common ancestor of the variola major circulating in the Old World between the 1940s and the 1970s most probably originated in the Far East in the first decades of the XX century, and then spread to Indian subcontinent in the 1920s. India represented a center of further spread of VARV to eastern Africa in the 1940s and to the Middle East in the 1960s. The phylogeographic scenario obtained by the maximum-likelihood based method was congruent with that obtained by Bayesian framework, but the analysis was faster indicating the usefulness of this method in the analyses of large viral genomes. Our results may help to explain the controversial reconstructions of the history of VARV obtained using long or short timescale for calibration.

Evolution and Taxonomic Significance of Seed Micromorphology in Impatiens (Balsaminaceae).

Impatiens is one of the most species-rich genera of angiosperms, with more than 1,000 species distributed in Eurasia and Africa. Previous studies have shown that seeds of Impatiens display enormous morphological diversity, and seed micromorphology may contribute to the classification of those species. However, the micromorphological seed coat characteristics of Impatiens seeds have not been systematically studied. In this study, we examined 117 Impatiens seeds from two subgenera and seven sections, and analyzed the seed characters of shape, primary ornamentation, secondary ornamentation, anticlinal cell wall, and periclinal cell wall. We discovered that, according to the different shapes of ornamentation, seed coat can be divided into three types, viz, reticulate type, protrusive type, appendicular type, and that they can be further subdivided into 10 subtypes. In addition, the characteristics of seed coat ornamentation with taxonomic significance in this genus are discussed. We reconstructed the ancestral states of the above seed characters of the Impatiens using the maximum likelihood approach based on the reconstructed phylogenetic framework. The seed character reconstruction showed that the seed shape, primary ornamentation, and anticlinal cell wall could be identified as unambiguous, while other characters were ambiguous in the last common ancestor of Impatiens. Reconstruction of important seed morphological characters showed that the secondary ornamentation possesses high plasticity, and the primary ornamentation has high homology. In addition, we inferred the evolutionary trends of seed ornamentation and found that the seed coat ornamentation of Impatiens experienced a complex evolutionary process from a reticulate type into more complex types. We also discussed the relationship between seed coat diversity vs. environmental adaptation and seed dispersal in Impatiens.

A well-supported nuclear phylogeny of Poaceae and implications for the evolution of C4 photosynthesis

Poaceae (the grasses) includes rice, maize, wheat, and other crops, and is the most economically important angiosperm family. Poaceae is also one of the largest plant families, consisting of over 11 000 species with a global distribution that contributes to diverse ecosystems. Poaceae species are classified into 12 subfamilies, with generally strong phylogenetic support for their monophyly. However, many relationships within subfamilies, among tribes and/or subtribes, remain uncertain. To better resolve the Poaceae phylogeny, we generated 342 transcriptomic and seven genomic datasets; these were combined with other genomic and transcriptomic datasets to provide sequences for 357 Poaceae species in 231 genera, representing 45 tribes and all 12 subfamilies. Over 1200 low-copy nuclear genes were retrieved from these datasets, with several subsets obtained using additional criteria, and used for coalescent analyses to reconstruct a Poaceae phylogeny. Our results strongly support the monophyly of 11 subfamilies; however, the subfamily Puelioideae was separated into two non-sister clades, one for each of the two previously defined tribes, supporting a hypothesis that places each tribe in a separate subfamily. Molecular clock analyses estimated the crown age of Poaceae to be ∼101 million years old. Ancestral character reconstruction of C3/C4 photosynthesis supports the hypothesis of multiple independent origins of C4 photosynthesis. These origins are further supported by phylogenetic analysis of the ppc gene family that encodes the phosphoenolpyruvate carboxylase, which suggests that members of three paralogous subclades (ppc-aL1a, ppc-aL1b, and ppc-B2) were recruited as functional C4ppc genes. This study provides valuable resources and a robust phylogenetic framework for evolutionary analyses of the grass family.

Genome size evolution of the extant lycophytes and ferns

Ferns and lycophytes have remarkably large genomes. However, little is known about how their genome size evolved in fern lineages. To explore the origins and evolution of chromosome numbers and genome size in ferns, we used flow cytometry to measure the genomes of 240 species (255 samples) of extant ferns and lycophytes comprising 27 families and 72 genera, of which 228 species (242 samples) represent new reports. We analyzed correlations among genome size, spore size, chromosomal features, phylogeny, and habitat type preference within a phylogenetic framework. We also applied ANOVA and multinomial logistic regression analysis to preference of habitat type and genome size. Using the phylogeny, we conducted ancestral character reconstruction for habitat types and tested whether genome size changes simultaneously with shifts in habitat preference. We found that 2C values had weak phylogenetic signal, whereas the base number of chromosomes (x) had a strong phylogenetic signal. Furthermore, our analyses revealed a positive correlation between genome size and chromosome traits, indicating that the base number of chromosomes (x), chromosome size, and polyploidization may be primary contributors to genome expansion in ferns and lycophytes. Genome sizes in different habitat types varied significantly and were significantly correlated with habitat types; specifically, multinomial logistic regression indicated that species with larger 2C values were more likely to be epiphytes. Terrestrial habitat is inferred to be ancestral for both extant ferns and lycophytes, whereas transitions to other habitat types occurred as the major clades emerged. Shifts in habitat types appear be followed by periods of genomic stability. Based on these results, we inferred that habitat type changes and multiple whole-genome duplications have contributed to the formation of large genomes of ferns and their allies during their evolutionary history.

Taming Dragons: The Buddhist Mythmaking of Sacred Violence in Medieval Buddhist Tales Samgukyusa and Konjaku Monogatarishū

The insights available in Japanese medieval Buddhist narratives on the appropriation and reconstruction of various non-Buddhist divine characters has long been overlooked. Yet an examination of these narratives reveals Buddhist thinkers’ endeavors to reconfigure the religious and cultural roles of folk religious worship and related figures into essential tools through which they could popularize Buddhism, legitimize Buddhist cosmology, and, ultimately, to dominate the religious and cultural milieu of medieval Japan. This essay compares such medieval Buddhist narratives of Japan with Korean mythic tale literature. It pays particular attention to representations of folk religious figures in the works, and in particular, the dragon, an exceptionally prominent character associated with particular roles and symbolism in the simplified, popularized Buddhist framework represented in the dragon character in Korean literature Samgukyusa (三國遺事) and Japanese Konjaku monogatarishū (今昔物語集). The essay investigates various representations of the dragon, which was apparently understood in ambivalent terms—as both a sacred figure and a being inferior to Buddhist figures. Moreover, the way in which such representation is related to medieval Japanese discourse of defilement and threatening power is illuminated. Consequently, the essay discusses how Buddhist mythographers in medieval Japan devised a sophisticated literary strategy to accommodate non-Buddhist religious symbols and, simultaneously, to marginalize them.

Phylogeny of Alpinia coriandriodora D. Fang and Implications for Character Evolution and Conservation.

Alpinia, the largest genus of Zingiberaceae, includes ca. 250 species. The A. coriandriodora D. Fang was recognized for Vietnamese flora. However, the systematic position of this species within Alpinia genus was unclear. The study aimed to understand the phylogenetic placement of A. coriandriodora based on the molecular data and interpret evolution of the key morphological characters. The phylogenetic analysis were conducted by using the combined dataset of two DNA regions by both Maximum Likelihood (ML) and Bayesian Inference (BI) methods. Seven morphological characters were selected for morphological character evolution and the analysis was performed in Mesquite. Alpinia coriandriodora was supported closely related to southern Chinese species of Alpinia. Morphological character optimizations suggest that the presence/absence of tomentum in leaf, inflorescence rachis and ovary is an important character for the taxonomy of Alpinia. The character evolution analyses indicated that panicle is ancestral character in Alpinia. The A. coriandriodora shares different evolutionary histories based on our character re-construction to most members of Southeast Asian Alpinia. The presence of filament is supposed to be an adaptation to the pollination by insects for species of Alpinia. The present study revealed the molecular phylogenetic relationship of A. coriandriodora within Alpinia. The presence of filament could be an adaptation to the pollination by insects for species of Alpinia. Some reasonable conservation strategies are proposed to protect the species including maintenance of the plant's natural habitats, seeds or seedlings collection for germplasm storage and artificial breeding using biotechnology.

An Extraordinary Rosette and Resurrection New Spikemoss, Selaginella iridescens (Selaginellaceae) from Hainan Island, China

Selaginella iridescens (Selaginellaceae), a new species of spikemoss from Hainan Island, China, is described based on morphological and molecular evidence. The new species morphologically resembles S. pseudotamariscina from Vietnam which was recently recognized and segregated from S. tamariscina and S. pulvinata. Some characters of S. iridescens, including the iridescent leaves and long arista (0.35–1.20 mm long), the widely membranaceous margin of axillary leaves (ca. 2/3), dorsal leaves sulcate extending to the top, and slender main stem, dorsoventrally prostrate, distinguish it from S. pseudotamariscina. Phylogenetic results based on rbcL of 28 Selaginella species indicate that S. iridescens is sister to S. pseudotamariscina, and distant from the S. tamariscina-S.pulvinata clade. The ancestral character reconstruction result reveals that the rosette is apomorphic and has evolved independently at least six times in Selaginella.

The effects of fossil taxa, hypothetical predicted ancestors, and a molecular scaffold on pseudoextinction analyses of extant placental orders.

Pseudoextinction analyses, which simulate extinction in extant taxa, use molecular phylogenetics to assess the accuracy of morphological phylogenetics. Previous pseudoextinction analyses have shown a failure of morphological phylogenetics to place some individual placental orders in the correct superordinal clade. Recent work suggests that the inclusion of hypothetical ancestors of extant placental clades, estimated by ancestral state reconstructions of morphological characters, may increase the accuracy of morphological phylogenetic analyses. However, these studies reconstructed direct hypothetical ancestors for each extant taxon based on a well-corroborated molecular phylogeny, which is not possible for extinct taxa that lack molecular data. It remains to be determined if pseudoextinct taxa, and by proxy extinct taxa, can be accurately placed when their immediate hypothetical ancestors are unknown. To investigate this, we employed molecular scaffolds with the largest available morphological data set for placental mammals. Each placental order was sequentially treated as pseudoextinct by exempting it from the molecular scaffold and recoding soft morphological characters as missing for all its constituent species. For each pseudoextinct data set, we omitted the pseudoextinct taxon and performed a parsimony ancestral state reconstruction to obtain hypothetical predicted ancestors. Each pseudoextinct order was then evaluated in seven parsimony analyses that employed combinations of fossil taxa, hypothetical predicted ancestors, and a molecular scaffold. In treatments that included fossils, hypothetical predicted ancestors, and a molecular scaffold, only 8 of 19 pseudoextinct placental orders (42%) retained the same interordinal placement as on the molecular scaffold. In treatments that included hypothetical predicted ancestors but not fossils or a scaffold, only four placental orders (21%) were recovered in positions that are congruent with the scaffold. These results indicate that hypothetical predicted ancestors do not increase the accuracy of pseudoextinct taxon placement when the immediate hypothetical ancestor of the taxon is unknown. Hypothetical predicted ancestors are not a panacea for morphological phylogenetics.

Geology of the Northern Apennines nappe stack on eastern Elba (Italy): new insights on the Neogene orogenic evolution of the Northern Tyrrhenian Sea

ABSTRACT We document the tectonic and metamorphic evolution of thrust nappes of the eastern island of Elba. The area exposes a natural cross section of the Northern Apennines hinterland, from the metamorphic basement units to the overlying continent- and ocean-derived nappes. We integrated mapping, analysis of structures and microstructures, and the interpretation of drill core logs with lithostratigraphic, metamorphic, and geochronological constraints, producing a novel geological map of eastern Elba (1:5’000 scale). We show that the area experienced polyphase Oligocene – Pliocene contractional tectonics marked by in-sequence and out-of-sequence thrusting accompanied by folding and overprinted by faulting in the Pliocene. Magmatism occurred during contraction with post-magmatic thrusting ultimately coupling HP-LT and LP-HT units. Drill core logs allow for the first time the reconstruction of the N-dipping character of the Zuccale Fault, which represents the youngest (late Miocene – early Pliocene) large-scale structure in the area.

Textual representation of emotions in Somerset Maugham’s “The Moon and Sixpence”

Somerset Maugham is one of the most “emotionally intense” authors in English literature. His greatest works always reveal the “inner life of the individual” (E. Etkind), a person’s susceptibility to various transformations under the influence of feelings and states (“Theater”, “Of Human Bondage”, “The Moon and Sixpence”). At the same time, the emotions being retransmitted when translating a literary text is one of the most difficult tasks in translation theory. As representatives of the architectonic to comprehend the world, emotions are always culturally specific and often do not have equivalents in another mentality and another language. Such are, for example, the English-language concepts (which, in turn, “explain” the emotion) “melancholia”, “blues” and others. The purpose of this work is to explain semantically the category of “emotionality” and understand its ideological and thematic significance in a literary text by comparing the material of two languages — the original English and Russian as the target language. The methods we have taken in the process of working on the text: descriptive, explanatory, emotion thematisation, denotative analysis, emotive analysis, hermeneutic, conceptual, and selective (method of sampling passionary couplings that is slots). Research hypothesis: The category of emotionality is involved in the reconstruction of characters’ images at the level of text perception (the theory of respondents). The means to retransmit emotions when translating a text depends on the mental attitudes of different ethnic groups, therefore, it is necessary to identify “intersection points” that are equally acceptable both for the original text and for its translation.

Cuban history of CRF19 recombinant subtype of HIV-1.

CRF19 is a recombinant form of HIV-1 subtypes D, A1 and G, which was first sampled in Cuba in 1999, but was already present there in 1980s. CRF19 was reported almost uniquely in Cuba, where it accounts for ∼25% of new HIV-positive patients and causes rapid progression to AIDS (∼3 years).We analyzed a large data set comprising ∼350 pol and env sequences sampled in Cuba over the last 15 years and ∼350 from Los Alamos database. This data set contained both CRF19 (∼315), and A1, D and G sequences. We performed and combined analyses for the three A1, G and D regions, using fast maximum likelihood approaches, including: (1) phylogeny reconstruction, (2) spatio-temporal analysis of the virus spread, and ancestral character reconstruction for (3) transmission mode and (4) drug resistance mutations (DRMs). We verified these results with a Bayesian approach. This allowed us to acquire new insights on the CRF19 origin and transmission patterns. We showed that CRF19 recombined between 1966 and 1977, most likely in Cuban community stationed in Congo region. We further investigated CRF19 spread on the Cuban province level, and discovered that the epidemic started in 1970s, most probably in Villa Clara, that it was at first carried by heterosexual transmissions, and then quickly spread in the 1980s within the “men having sex with men” (MSM) community, with multiple transmissions back to heterosexuals. The analysis of the transmission patterns of common DRMs found very few resistance transmission clusters.Our results show a very early introduction of CRF19 in Cuba, which could explain its local epidemiological success. Ignited by a major founder event, the epidemic then followed a similar pattern as other subtypes and CRFs in Cuba. The reason for the short time to AIDS remains to be understood and requires specific surveillance, in Cuba and elsewhere.

Molecular Phylogeny, Character Evolution, and Biogeography of Hydrangea Section Cornidia, Hydrangeaceae.

Background: Hydrangea section Cornidia consists of 26 currently accepted species and a yet undefined number of new species and erroneously synonymized taxa. This clade consists of (sub)tropical lianas occurring from northern Mexico to southern Chile and Argentina, and one species from Southeast Asia. Currently, no molecular phylogenetic hypothesis is available that includes more than a few species of this section. Hence, a resolved and well-sampled molecular phylogenetic hypothesis may help to enforce taxonomic decisions. In this study, we present a phylogenetic framework based on sequences from two low copy nuclear genes from a comprehensive taxon sampling of H. section Cornidia and a selection of outgroups. Our phylogenetic reconstructions prove the non-monophyly of the traditionally recognized subsections Monosegia and Polysegia and their corresponding series, Speciosae and Aphananthae, and Synstyleae and Chorystyleae, respectively. Three morphologically defined species were recovered with high support as monophyletic, namely, Hydrangea panamensis, Hydrangea serratifolia, and Hydrangea tarapotensis. However, statistical support for some shallow nodes did not allow to refute, with high support, the monophyly of several of the herein recognized species for which more than one individual could be analyzed. Based on the obtained phylogenetic framework, we reconstructed the evolution of selected reproductive characters. Hydrangea section Cornidia is the only genus section for which dioecism has been extensively documented. Our character reconstruction of sexual dimorphism shows that dioecism is the ancestral state in this section and that this was reversed to monoecy in Hydrangea seemannii and Hydrangea integrifolia. Character reconstruction for the enlarged marginal flowers recovered their presence as the ancestral character state in H. section Cornidia, although at least three internal lineages independently lost them; thus, losses were reconstructed to be more likely than gain. With respect to the flower color, more species exhibit white than red flowers, and white is reconstructed as the ancestral state. Cornidia also shows an unusual disjunct geographic distribution between Asia and Central Mesoamerica—South America, as it is not present in the USA and Canada. The origin of Cornidia is reconstructed to be the New World with higher probability, and the presence of one species in Asia is likely due to long-distance dispersal.

Fast, efficient, and accurate dielectric screening using a local real-space approach.

Various many-body perturbation theory techniques for calculating electron behavior rely on W, the screened Coulomb interaction. Computing W requires complete knowledge of the dielectric response of the electronic system, and the fidelity of the calculated dielectric response limits the reliability of predicted electronic and structural properties. As a simplification, calculations often begin with the random-phase approximation (RPA). However, even RPA calculations are costly and scale poorly, typically as N 4 (N representing the system size). A local approach has been shown to be efficient while maintaining accuracy for screening core-level excitations [Ultramicroscopy 106, 986 (2006)]. We extend this method to valence-level excitations. We present improvements to the accuracy and execution of this scheme, including reconstruction of the all-electron character of the pseudopotential-based wave functions, improved N 2 log N scaling, and a parallelized implementation. We discuss applications to Bethe-Salpeter equation calculations of core and valence spectroscopies.