Miracle-dz/UniFAR-FTUs huggingface dataset:
Orthogonal Decomposition of the Genetic Variance for Epistatic Traits Under Linkage Disequilibrium—Applications to the Analysis of Bateson-Dobzhansky-Müller Incompatibilities and Sign Epistasis

The one-century-old theory of orthogonal genetic variance decomposition originated the field of quantitative genetics and has kept on being improved ever since. Recently, serious concerns about the possibility of attaining a satisfactory implementation of genetic variance decomposition with linkage disequilibrium (LD) and epistasis have been raised. In this paper we dissipate such doubts by completing the classical theory of variance decomposition into additive, dominance and epistasis components with LD. We apply that theory to the analysis of the genotype-to-phenotype maps of two cases of particular evolutionary interest—Bateson-Dobzhansky-Müller incompatibilities and sign epistasis. For the first case we show how negative LD and reduction of heterozygotes may contribute to maintain genetic variability after secondary contact. For the second case we show that LD transforms the set of frequencies leading to an evolutionary plateau into a ridge. Our theoretical developments reassuringly reflect the complexity LD conveys to genetic systems throughout novel properties—as compared with systems under linkage equilibrium. We argue that such particularities might have actually contributed to cause confusion about the feasibility of developing this methodology. In any case, the theory we provide in this paper enables new perspectives in both evolutionary and quantitative genetics studies.
Fungal Community Ecology Using MALDI-TOF MS Demands Curated Mass Spectral Databases

Authors thank professors Marc-Andre Lachance and GregThorn for critical reading on initial drafts of this piece. Mariana Cereia, English teacher, kindly proofread the ﬁnal version. Authors also thank Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP), Conselho de Desenvolvimento Cientiﬁco e Tecnologico (CNPq) and National System for Research on Biodiversity (Sisbiota-Brazil, CNPq 563260/2010-6/FAPESP n◦ 2010/52322-3) for supporting previous work that led to this opinion piece. CS thanks the Universidad de La Frontera (Temuco, Chile) for the partial funding from Project DIUFRO DI18-0121. NL thanks the partial support by the Portuguese Foundation for Science and Technology (FCT), the strategic funding of the UID/BIO/04469/2019 unit, COMPETE 2020 (POCI-01-0145-FEDER-006684) and the BioTecNorte operation (NORTE-01-0145-FEDER-000004), funded by the European Regional Development Fund through Norte2020—Programa Operacional Regional do Norte.
Distributed Online Learning of Fog Computing Under Nonuniform Device Cardinality

Processing data around the point of capture, fog computing can support computationally demanding Internet-of-Things (IoT) services. Distributed online optimization is important given the size of IoT, but challenging due to time variations of random traffic and nonuniform connectivity (or cardinality) of edge servers and IoT devices. This paper presents a distributed online learning approach to asymptotically minimizing the time-average cost of fog computing in the absence of the a-priori knowledge on traffic randomness, for light-weight, and delay-tolerant application scenarios. Stochastic gradient descent is exploited to decouple the optimizations between time slots. A graph matching problem is then formulated for every time slot by decoupling and unifying the nonuniform cardinalities, and solved in a distributed manner by developing a new linear (1/2)-approximation method. We prove that the optimality loss resulting from the distributed approximate graph matching method can be compensated and diminish by increasing the learning time. Corroborated by simulations, the proposed distributed online learning is asymptotically optimal and superior to the state of the art in terms of throughput and energy efficiency.
Formal Modeling and Verification of a Victim DRAM Cache

The emerging Die-stacking technology enables DRAM to be used as a cache to break the “Memory Wall” problem. Recent studies have proposed to use DRAM as a victim cache in both CPU and GPU memory hierarchies to improve performance. DRAM caches are large in size and, hence, when realized as a victim cache, non-inclusive design is preferred. This non-inclusive design adds significant differences to the conventional DRAM cache design in terms of its probe, fill, and writeback policies. Design and verification of a victim DRAM cache can be much more complex than that of a conventional DRAM cache. Hence, without rigorous modeling and formal verification, ensuring the correctness of such a system can be difficult. The major focus of this work is to show how formal modeling is applied to design and verify a victim DRAM cache. In this approach, we identify the agents in the victim DRAM cache design and model them in terms of interacting state machines. We derive a set of properties from the specifications of a victim cache and encode them using Linear Temporal Logic. The properties are then proven using symbolic and bounded model checking. Finally, we discuss how these properties are related to the dataflow paths in a victim DRAM cache.
Hexokinase and Glucokinases Are Essential for Fitness and Virulence in the Pathogenic Yeast Candida albicans

Metabolic flexibility promotes infection and commensal colonization by the opportunistic pathogen Candida albicans. Yeast cell survival depends upon assimilation of fermentable and non-fermentable locally available carbon sources. Physiologically relevant sugars like glucose and fructose are present at low level in host niches. However, because glucose is the preferred substrate for energy and biosynthesis of structural components, its efficient metabolization is fundamental for the metabolic adaptation of the pathogen. We explored and characterized the C. albicans hexose kinase system composed of one hexokinase (CaHxk2) and two glucokinases (CaGlk1 and CaGlk4). Using a set of mutant strains, we found that hexose phosphorylation is mostly assured by CaHxk2, which sustains growth on hexoses. Our data on hexokinase and glucokinase expression point out an absence of cross regulation mechanisms at the transcription level and different regulatory pathways. In the presence of glucose, CaHxk2 migrates in the nucleus and contributes to the glucose repression signaling pathway. In addition, CaHxk2 participates to oxidative, osmotic and cell wall stress responses, while glucokinases are overexpressed under hypoxia. Hexose phosphorylation is a key step necessary for filamentation, that is affected in the hexokinase mutant. Virulence of this mutant is clearly impacted in the Galleria mellonella and macrophage models. Filamentation, glucose phosphorylation and stress response defects of the hexokinase mutant prevent host killing by C. albicans. By contributing to metabolic flexibility, stress answer response and morphogenesis, hexose kinase enzymes play an essential role in the virulence of C. albicans. Author summary The pathogenic yeast C. albicans is both a powerful commensal and pathogen of humans that can infect wide range of organs and body sites. To grow in its host and establish an infection, the pathogen must assimilate carbon from these heterogenous environments. C. albicans regulates central carbon metabolism in a niche-specific manner, activating alternatively gluconeogenesis, glyoxylate cycle and the glycolytic metabolism. For yeast and other microorganisms, glucose is the preferred carbon and energy source and its accurate detection and metabolism is essential. However, the glycolytic hexose kinase system has not been investigated yet in C. albicans. In this report, we showed that hexokinase and glucokinases contribute to the fitness and virulence of C. albicans. We revealed the main metabolic role of the hexokinase CaHxk2 which impacts on growth, glucose signalling, morphological transition and virulence. However, glucokinases contribute to the anoxic response and their implication in regulation processes is suggested.
Phylogeography of Schisandra chinensis (Magnoliaceae) Reveal Multiple Refugia With Ample Gene Flow in Northeast China

Temperate conifers and broadleaved mixed forests in northeast China are ideal to investigate the genetic consequences of climate changes during the last glacial maximum (LGM), 29 – 16 kya. As previous studies were focused on tree species with long generation time; here, the evolutionary history of Schisandra chinensis, a climber species with a generation time of five years, was investigated using chloroplast DNA (cpDNA), nuclear single copy gene (nSCG), and nuclear single sequence repeats (nSSRs, i.e., microsatellite) markers, along with ecological niche modeling (ENM), which predicted a suitable habitat in Korea Peninsula (KP) during the LGM. Private haplotypes and high genetic diversity of both cpDNA and nSCG were mainly found in KP and Changbai Mt. (CB). Although no significant phylogeographic structure was detected in the cpDNA and nSCG, three nSSRs clusters roughly distributed in west (CB and KP), east (north China), and north (Xiaoxing’an Range, XR) regions were found in Structure analysis. The approximate Bayesian computation analysis showed the west cluster diverged at 35.45 kya, and the other two clusters at 19.85 kya. The genetic diversity calculated for each of the three markers showed no significant correlation with latitude. Genetic differentiation of nSSRs was also not correlated with geographic distance. Migrate analysis estimated extensive gene flow between almost all genetic cluster pairs and BOTTLENECK analysis showed that few populations experienced severe bottlenecks. Overall, results indicate that S. chinensis survived the LGM in situ in multiple refugia, which likely include two macrorefugia (KP and CB) and two microrefugia (XR and north China). Extensive postglacial gene flow among the three nSSRs clusters led to uniformly distributed genetic diversity and low genetic differentiation.
Confidential Broadcasting and Service Integration in Millimeter Wave Systems

This paper focuses on the transmit design for efficient implementation of confidential broadcasting and service integration in a two-receiver millimeter wave (mmWave) system. In confidential broadcasting, a transmitter broadcasts two confidential messages to two receivers. Each confidential message is intended for one specified receiver and kept perfectly secret from the other. To fully exploit the propagation characteristics of mmWave channels, two heuristic transmit schemes, i.e., matched filter (MF) and partially MF (PMF) schemes, are proposed to tradeoff the secrecy rates at the two receivers. We obtain the secrecy rate regions by varying a power allocation ratio. On the other hand, in service integration, a multicast message intended for both receivers is introduced in the system. With MF and PMF schemes used for confidential message transmission, we further consider the beamforming design of the multicast message, such that the achievable multicast rate is maximized. The associated optimization problem admits a closed-form solution, and then the secrecy rate region can be obtained still by varying a power allocation ratio. We also compare our proposal with the globally optimal schemes in terms of achievable performance and implementation complexity. Finally, numerical results are presented to verify the efficacy of our proposed method.
Sequential Relay Selection in D2D-Enabled Cellular Networks With Outdated CSI Over Mixed Fading Channels

The impact of outdated channel state information on two sequential relay selection schemes for device-to-device underlaid cellular networks over mixed fading channels is investigated. To this end, the mutual outage probability (MOP) is analyzed in which an easy-to-evaluate analytical expression for the MOP is derived. Moreover, an asymptotic analysis of the MOP at high signal-to-noise ratio is provided, and the diversity order is evaluated.
Frugivory and Seed Dispersal by Lizards: A Global Review

Birds and mammals are the only vertebrates which receive comprehensive attention in studies of dispersal of fleshy-fruited plant species. However, recently the importance of fleshy fruit in the diet of lizards (order Squamata: suborder Sauria), and the role of lizards as seed dispersers have been recognized in a number of studies, especially in studies from arthropod-poor habitats such as oceanic islands. Here, we revisit the evidence of fruit-eating lizards on a global scale in order to test if fruit consumption is more common on islands than expected by chance. We constructed a database of 470 lizard species (from a global count of 6,515 species), that have been reported to consume fleshy fruits. This set of lizards belong to 27 families with Scincidae (N= 78 species), Gekkonidae (69), and Dactyloidae (55) having more frugivorous species than other lizard families. We found that 62.4% of these lizards inhabit islands, whereas only one third (35.3%) of all lizard species inhabit on islands. These values support the presence of an ‘insular phenomenon’, however, we also tested if this biogeographical pattern might be driven by body size and evolutionary history of lizards. Thus, we looked for any phylogenetic signals in the distributions of lizard body size, island-presence, and frugivory and calculated phylogenetically corrected correlations among the three variables on a global subset of 2,417 lizard species for which we had detailed phylogenetic information. Both lizard body size and island-presence were weakly influenced by phylogeny; whereas, frugivory was not. In addition, we found that (1) body size and frugivory were weakly positively correlated; (2) body size and island-presence were uncorrelated; and (3) island-presence and frugivory were strongly positively correlated. Thus, we conclude that the main driver of frugivory on islands is the specific island environment and not lizard body size per se. Islands are said to be poor in arthropods and predators, and this may force/allow island lizards to forage for additional food sources such as fleshy fruits. We also suggest that modern lizards as well as their ancestors may potentially play an important role to many plants as seed dispersers.
Citation.js: a format-independent, modular bibliography tool for the browser and command line

Background Given the vast number of standards and formats for bibliographical data, any program working with bibliographies and citations has to be able to interpret such data. This paper describes the development of Citation.js (https://citation.js.org/), a tool to parse and format according to those standards. The program follows modern guidelines for software in general and JavaScript in specific, such as version control, source code analysis, integration testing and semantic versioning. Results The result is an extensible tool that has already seen adaption in a variety of sources and use cases: as part of a server-side page generator of a publishing platform, as part of a local extensible document generator, and as part of an in-browser converter of extracted references. Use cases range from transforming a list of DOIs or Wikidata identifiers into a BibTeX file on the command line, to displaying RIS references on a webpage with added Altmetric badges to generating ”How to cite this” sections on a blog. The accuracy of conversions is currently 27% for properties and 60% for types on average and a typical initialization takes 120 ms in browsers and 1 s with Node.js on the command line. Conclusions Citation.js is a library supporting various formats of bibliographic information in a broad selection of use cases and environments. Given the support for plugins, more formats can be added with relative ease.
Codebook-Based Hybrid Beamforming Design for MISOME Wiretap Channel

For practical implementation of multi-input multi-output systems, hybrid analog-digital beamforming may address the challenges of hardware limitation in fully digital beamforming (FDB). In this letter, in order to tackle the potential security issues in large-scale multi-antenna systems without exorbitant hardware cost, we focus on the codebook-based hybrid beamforming design in multi-input single-output multi-eavesdropper Gaussian wiretap channel to maximize the secrecy rate. However, the secrecy rate maximization (SRM) problem is non-convex by nature due to the codebook constraint imposed by analog beamforming. To handle it, we first reformulate the SRM problem into a combinatorial inner product maximization problem. Then, a combinatorial matching pursuit algorithm is proposed to solve this problem, in which the analog beamformer is designed independently of the digital beamformer. With the obtained analog beamformer, we show that the optimal digital beamformer admits a closed-form expression. Simulation results reveal that the proposed algorithm, though suffering from the inherent precision loss of the codebook, can achieve the near-optimal performance of the optimal FDB.
Progress and Opportunities in the Characterization of Cellulose – An Important Regulator of Cell Wall Growth and Mechanics

The plant cell wall is a dynamic network of several biopolymers and structural proteins including cellulose, pectin, hemicellulose and lignin. Cellulose is one of the main load bearing components of this complex, heterogeneous structure, and in this way, is an important regulator of cell wall growth and mechanics. Glucan chains of cellulose aggregate via hydrogen bonds and van der Waals forces to form long thread-like crystalline structures called cellulose microfibrils. The shape, size, and crystallinity of these microfibrils are important structural parameters that influence mechanical properties of the cell wall and these parameters are likely important determinants of cell wall digestibility for biofuel conversion. Cellulose–cellulose and cellulose-matrix interactions also contribute to the regulation of the mechanics and growth of the cell wall. As a consequence, much emphasis has been placed on extracting valuable structural details about cell wall components from several techniques, either individually or in combination, including diffraction/scattering, microscopy, and spectroscopy. In this review, we describe efforts to characterize the organization of cellulose in plant cell walls. X-ray scattering reveals the size and orientation of microfibrils; diffraction reveals unit lattice parameters and crystallinity. The presence of different cell wall components, their physical and chemical states, and their alignment and orientation have been identified by Infrared, Raman, Nuclear Magnetic Resonance, and Sum Frequency Generation spectroscopy. Direct visualization of cell wall components, their network-like structure, and interactions between different components has also been made possible through a host of microscopic imaging techniques including scanning electron microscopy, transmission electron microscopy, and atomic force microscopy. This review highlights advantages and limitations of different analytical techniques for characterizing cellulose structure and its interaction with other wall polymers. We also delineate emerging opportunities for future developments of structural characterization tools and multi-modal analyses of cellulose and plant cell walls. Ultimately, elucidation of the structure of plant cell walls across multiple length scales will be imperative for establishing structure-property relationships to link cell wall structure to control of growth and mechanics.
Viability of Fee-Based Email Service for Retail Customers

Unsecure free email services face possible threats from spam, phishing, and hacking. Secure email eliminates most of these risks. The primary objective of this study was to understand the market for fee-based secure email service. A Web-based survey was designed using secondary research and inputs from focus group interviews and administered to a random sample of individuals living in the US. Analysis of data gathered from 189 responses revealed that although people are concerned about email security, they may be unwilling to purchase fee-based secure email service. Market for fee-based secure email service is small and dispersed throughout the US. Results also indicate that pricing drives individual intention to purchase fee-based email service. A scale to measure effectiveness of email service was developed. The study concludes the lack of a profitable market for the fee-based secure email service and discusses the challenges of marketing this service in a B-2-(2C) environment.
Identification of Key lncRNAs Associated With Atherosclerosis Progression Based on Public Datasets

Atherosclerosis is one of the most common type of cardiovascular disease and the prime cause of mortality in the aging population worldwide. However, the detail mechanisms and special biomarkers of atherosclerosis remain to be further investigated. Lately, long non-coding RNAs (lncRNAs) has attracted much more attention than other types of ncRNAs. In our work, we found and confirmed differently expressed lncRNAs and mRNAs in atherosclerosis by analyzing GSE28829. We performed the weighted gene co-expression network analysis (WGCNA) by analyzing GSE40231 to confirm highly correlated genes. Gene Ontology (GO) analysis were utilized to assess the potential functions of differential expressed lncRNAs in atherosclerosis. Co-expression networks were also constructed to confirm hub lncRNAs in atherosclerosis. A total of 5784 mRNAs and 654 lncRNAs were found to be dysregulated in the progression of atherosclerosis. A total of 15 lncRNA-mRNA co-expression modules were identified in this study based on WGCNA analysis. Moreover, a few lncRNAs, such as ZFAS1, LOC100506730, LOC100506691, DOCK9-AS2, RP11-6I2.3, LOC100130219, were confirmed as important lncRNAs in atherosclerosis. Taken together, bioinformatics analysis revealed these lncRNAs were involved in regulating the leukotriene biosynthetic process, gene expression, actin filament organization, t-circle formation, antigen processing, and presentation, interferon-gamma-mediated signaling pathway, and activation of GTPase activity. We believed that this study would provide potential novel therapeutic and prognostic targets for atherosclerosis.
Mechanical Conflicts in Twisting Growth Revealed by Cell-Cell Adhesion Defects

Many plants grow organs and tissues with twisted shapes. Arabidopsis mutants with impaired microtubule dynamics exhibit such a phenotype constitutively. Although the activity of the corresponding microtubule regulators is better understood at the molecular level, how large-scale twisting can emerge in the mutants remains largely unknown. Classically, oblique cortical microtubules would constrain the deposition of cellulose microfibrils in cells, and such conflicts at the cell level would be relaxed at the tissue scale by supracellular torsion. This model implicitly assumes that cell-cell adhesion is a key step to transpose local mechanical conflicts into a macroscopic twisting phenotype. Here we tested this prediction using the quasimodo1 mutant, which displays cell-cell adhesion defects. Using the spriral2/tortifolia1 mutant with hypocotyl helical growth, we found that qua1-induced cell-cell adhesion defects restore straight growth in qua1-1 spr2-2. Detached cells in qua1-1 spr2-2 displayed helical growth, confirming that straight growth results from the lack of mechanical coupling between cells rather than a restoration of SPR2 activity in the qua1 mutant. Because adhesion defects in qua1 depend on tension in the outer wall, we also showed that hypocotyl twisting in qua1-1 spr2-2 could be restored when decreasing the matrix potential of the growth medium, i.e., by reducing the magnitude of the pulling force between adjacent cells, in the double mutant. Interestingly, the induction of straight growth in qua1-1 spr2-2 could be achieved beyond hypocotyls, as leaves also displayed a flat phenotype in the double mutant. Altogether, these results provide formal experimental support for a scenario in which twisted growth in spr2 mutant would result from the relaxation of local mechanical conflicts between adjacent cells via global organ torsion.