Miracle-dz/UniFAR-FTUs huggingface dataset:
Polyploidy and Genome Evolution in Plants This Review Comes from a Themed Issue on Genome Studies and Molecular Genetics Edited

Genome doubling (polyploidy) has been and continues to be a pervasive force in plant evolution. Modern plant genomes harbor evidence of multiple rounds of past polyploidization events, often followed by massive silencing and elimination of duplicated genes. Recent studies have refined our inferences of the number and timing of polyploidy events and the impact of these events on genome structure. Many polyploids experience extensive and rapid genomic alterations, some arising with the onset of polyploidy. Survivorship of duplicated genes are differential across gene classes, with some duplicate genes more prone to retention than others. Recent theory is now supported by evidence showing that genes that are retained in duplicate typically diversify in function or undergo subfunctionalization. Polyploidy has extensive effects on gene expression, with gene silencing accompanying polyploid formation and continuing over evolutionary time. Introduction Among the more illuminating realizations to emerge from the genomics era has been the extent to which genome doubling (polyploidy) has been a pervasive force in plant evolution. Analyses of whole-genome sequences, extensive expressed sequence tag (EST) sets, and duplicated genomic regions have led to the realization that genome doubling has occurred repeatedly during plant evolution and that even plants with relatively small genomes, such as Arabidopsis thaliana, have been impacted by polyploidy [1,2]. Recent studies convincingly demonstrate that poly-ploidy entails far more than the mere merger of two genomes who passively acquiesce to their sudden collaboration , but instead involves a whole spectrum of molecular and physiological adjustments. Extensive genomic rearrangements, including exchanges between genomes and gene loss, often arise with the onset of polyploidiza-tion [3 ]. Genome doubling also significantly effects gene expression, resulting in epigenetically induced gene silencing [4,5]. Novel phenotypes are known to emerge from this genomic amalgam, including some with high visibility to natural selection, such as organ size and flowering time. Thus, polyploidy is a prominent and significant force in plant evolution, at temporal scales ranging from ancient to contemporary, and with profound effects at scales ranging from molecular to ecological. In this review, we draw attention to some of the more surprising and important recent advances in our understanding of polyploidy that have arisen from numerous studies, providing a gateway to the recent literature in the process. Polyploidy is an ancient and recurrent process leading to differential gene loss Several studies have revealed that multiple rounds of polyploidy have occurred during angiosperm evolution. Empirical observations come from diverse …
Considering both intra-pattern and inter-pattern anomalies for intrusion detection

Various approaches have been proposed to discover patterns from system call trails of UNIX processes to better model application behavior. However, these techniques only consider the relationship between system calls (or system audit events). We first refine the definition of maximal patterns given in (Wespi et al., 2000) and provide a pattern extraction algorithm to identify such maximal patterns. We then add one additional dimension to the problem domain by also taking into consideration the overlap relationship between patterns. We argue that an execution path of an application is usually not an arbitrary combination of various patterns; but rather, they overlap each other in some specific order. Such overlap relationship characterizes the normal behavior of the application. Finally, a novel pattern matching module is proposed to detect intrusions based on both intra-pattern and inter-pattern anomalies. We test this idea using the data sets obtained from the University of New Mexico. The experimental results indicate that our scheme detects significantly more anomalies than the scheme presented in (Wespi et al., 2000) while maintaining a very low false alarm rate.
Isolation and Characterization of Carinactivase, a Novel Prothrombin Activator in Echis carinatus Venom with a Unique Catalytic Mechanism (*)

The venom of the viper Echis carinatus contains a metalloprotease, ecarin, that is a potent prothrombin activator. We here show that the venom is also rich in another prothrombin activator, which does not belong to any known category of prothrombin activators. The novel enzyme, designated carinactivase-1 (CA-1), consists of two subunits held together non-covalently but very tightly. One subunit is a 62-kDa polypeptide that has metalloprotease activity and is homologous to the single-chain enzyme ecarin; the other subunit of 25 kDa consists of two disulfide-linked polypeptides of 17 and 14 kDa, and this subunit resembles the anticoagulant in the habu snake venom, IX/X-bp, that specifically binds the Gla domains of coagulation factors IX and X in a Ca-dependent fashion. The activation of prothrombin by CA-1 requires Ca ions at millimolar concentrations and in the absence of Ca ions this enzyme is virtually inactive. By contrast, activation by ecarin is completely independent of Ca ions. CA-1, unlike ecarin, does not activate prothrombin derivatives, in which binding of Ca ions has been perturbed, namely prethrombin-1 and acarboxyprothrombin. Furthermore, the isolated catalytic subunit, although its activity is greatly reduced as compared to that of the holoenzyme, no longer requires Ca ions for the activation of prothrombin. Reconstitution with the non-catalytic 25-kDa subunit restores high level activity and the dependence on Ca ions. Finally, prothrombin activation by CA-1 is inhibited by prothrombin fragment 1, and the isolated non-catalytic subunit is capable of binding fragment 1 in the presence of Ca ions. From these observations, we postulate the following unique mechanism for the activation of prothrombin by CA-1. The enzyme primarily recognizes the Ca-bound conformation of the Gla domain in prothrombin via the 25-kDa regulatory subunit, and the subsequent conversion of prothrombin to active thrombin is catalyzed by the 62-kDa catalytic subunit.
Analyzing and Enhancing Dynamic Threshold Policy of Data Center Switches

Today’s data center switches usually employ on-chip shared memory; buffer management policy in them is essential to ensure fair sharing of memory among all ports. Among various polices, Dynamic Threshold (DT) policy is widely used by switch vendors. Meanwhile, in data centers, distributed applications such as MapReduce often introduce micro-burst traffic into network and the packet dropping caused by micro-burst usually leads to serious performance degradation. When micro-burst traffic arrives at switches, DT is unable to fully utilize the buffer to absorb it. Therefore, in this paper, we theoretically deduce the sufficient conditions for packet dropping caused by micro-burst traffic, and quantitatively estimate the free buffer size when packets are dropped. The results show that the free buffer size can be very large when the number of overloaded ports is small. What’s worse, to ensure fair sharing of memory among output ports, packets from micro-burst traffic may be dropped even when the traffic size is much smaller than the buffer size. In light of these results, we propose the Enhanced Dynamic Threshold (EDT) policy, which can alleviate packet dropping caused by micro-burst traffic through fully utilizing the switch buffer and temporarily relaxing the fairness constraint. The simulation results show that EDT can absorb more micro-burst traffic than DT.
Eigenvalue statistics and lattice points

One of the more challenging problems in spectral theory and mathematical physics today is to understand the statistical distribution of eigenvalues of the Laplacian on a compact manifold. There are now several challenging conjectures about these, originating in the physics literature. In this survey, a version of a talk delivered as the Colloquio De Giorgi at the Scuola Normale Superiore of Pisa in May 2006, I will describe what is conjectured and what is known the very simple case of the flat torus, where the problems amount to counting lattice points in annuli and have a definite arithmetic flavour. Eigenvalue problems. Let M be a smooth, compact Riemannian manifold, the Laplace-Beltrami operator associated with the metric. We consider the eigenvalue problem ψ + λψ = 0, ψ ∈ L(M). As is well known, the spectrum is a discrete set of points, which we denote by 0 = λ0 ≤ λ1 ≤ λ2 ≤ . , whose only accumulation point is at infinity, and there is an orthonormal basis of L2(M) consisting of eigenfunctions. Example 1.1. The circle M = R/Z with the standard flat metric: the Laplacian is simply d2/dx2, as a basis for the eigenfunctions we may take sin 2πkx , cos 2πkx (k > 0) with eigenvalues 4π2k2 (each having multiplicity 2), together with the constant function 1 (eigenvalue zero). Example 1.2. The flat torus R2/Z2: here the Laplacian is = ∂2 ∂x2 + ∂2 ∂y2 and as an orthonormal basis of eigenfunctions we may take the exponentials exp(2π ik · x), k ∈ Z2, with eigenvalue 4π2|k|2. Spectral counting functions. We define the following spectral functions: A cumulative count n(x) := #{m : √λm ≤ x} Supported by a grant from the Israel Science Foundation.
Contribuição da Unidade Educacional Sistematizada na formação do enfermeiro Contribution of Educational Unit Systematized in nursing education

Resumo — O Curso de Enfermagem da Famema, de forma pioneira no Brasil, utiliza Aprendizagem Baseada em Problemas. Seu Projeto Pedagogico e pautado nas Diretrizes Curriculares Nacionais, sendo integrado e orientado por competencia dialogica. Objetivo: analisar a contribuicao da Unidade Educacional Sistematizada (UES) para formacao profissional e subsidiar a gestao no planejamento educacional. Pesquisa de natureza ex-post-facto com abordagem qualitativa, foram analisados depoimentos da avaliacao de uma amostra intencional, utilizando o Metodo de Analise de Conteudo na Modalidade Tematica. Identificou-se que a proposta da UES contribuiu para a aprendizagem ativa e critico reflexiva. Potencialidades desta organizacao: satisfacao com a metodologia, trabalho em grupo e correlacao entre os cenarios de aprendizagem. Dificuldades: terminalidade do estudo para serie e adaptacao a nova metodologia. Estes aspetos devem ser considerados para a melhoria educacional nessa instituicao. Palavras Chave - curriculo; enfermagem; avaliacao educacional; aprendizagem baseada em problemas.
Non-Orthogonal Multiple Access for Multiple-Antenna Relaying Networks

In this letter, we design non-orthogonal multiple access (NOMA) for multiple-antenna relaying networks. The receive antennas at the mobile users are assumed to adopt maximal ratio combining (MRC), whereas the transmit antenna that maximizes the instantaneous signal-to-noise ratio (SNR) at the relay is selected. The system outage performance is investigated and closed-form expressions for the exact outage probability are derived. Furthermore, we obtain the lower bound of the outage probability. Finally, simulation results are presented to show the correctness of the theoretical analysis and the superiority of NOMA.
Distinguishing between Incomplete Lineage Sorting and Genomic Introgressions: Complete Fixation of Allospecific Mitochondrial DNA in a Sexually Reproducing Fish (Cobitis; Teleostei), despite Clonal Reproduction of Hybrids

Distinguishing between hybrid introgression and incomplete lineage sorting causing incongruence among gene trees in that they exhibit topological differences requires application of statistical approaches that are based on biologically relevant models. Such study is especially challenging in hybrid systems, where usual vectors mediating interspecific gene transfers - hybrids with Mendelian heredity - are absent or unknown. Here we study a complex of hybridizing species, which are known to produce clonal hybrids, to discover how one of the species, Cobitis tanaitica, has achieved a pattern of mito-nuclear mosaic genome over the whole geographic range. We appplied three distinct methods, including the method using solely the information on gene tree topologies, and found that the contrasting mito-nuclear signal might not have resulted from the retention of ancestral polymorphism. Instead, we found two signs of hybridization events related to C. tanaitica; one concerning nuclear gene flow and the other suggested mitochondrial capture. Interestingly, clonal inheritance (gynogenesis) of contemporary hybrids prevents genomic introgressions and non-clonal hybrids are either absent or too rare to be detected among European Cobitis. Our analyses therefore suggest that introgressive hybridizations are rather old episodes, mediated by previously existing hybrids whose inheritance was not entirely clonal. Cobitis complex thus supports the view that the type of resulting hybrids depends on a level of genomic divergence between sexual species.
Health benefits of legumes and pulses with a focus on Australian sweet lupins.

BACKGROUND AND OBJECTIVES The 68th United Nations General Assembly declared 2016 the International Year of Pulses. Therefore it is timely to review the current evidence of the benefits of legumes for human health with a focus on Australian sweet lupins. METHODS AND STUDY DESIGN Medline, Pubmed, Cochrane library were searched to identify cross-sectional/epidemiological studies, randomised controlled trials (RCTs) and systematic reviews. RESULTS The strongest evidence appears to be for links between eating legumes and reduced risk of colorectal cancer as well as eating soy foods and reduced LDL cholesterol. However, epidemiological studies and RCTs suggest that replacing several meat-based meals a week with legumes can have a positive impact on longevity, diabetes, cardiovascular disease and weight management, potentially via favourable effects on the gut microbiome. Sweet lupins are unique among legumes with one of the highest combined amounts of digestible plant protein (38%) and dietary fibre (30%). Unlike other legumes, their low amount of anti-nutritional factors negates the need for soaking/cooking and they can therefore be eaten uncooked. Sweet lupins may lower blood pressure, improve blood lipids and insulin sensitivity and favourably alter the gut microbiome. There is growing interest in pulses, especially sweet lupins, as ingredients to improve the nutritional value of baked goods (particularly gluten free) and to create novel products to replace meat. CONCLUSION Legumes form part of most traditional diets. They, including sweet lupins, can play a useful role in health maintenance.
HDAC Activity Is Required during Xenopus Tail Regeneration

The ability to fully restore damaged or lost organs is present in only a subset of animals. The Xenopus tadpole tail is a complex appendage, containing epidermis, muscle, nerves, spinal cord, and vasculature, which regenerates after amputation. Understanding the mechanisms of tail regeneration may lead to new insights to promote biomedical regeneration in non-regenerative tissues. Although chromatin remodeling is known to be critical for stem cell pluripotency, its role in complex organ regeneration in vivo remains largely uncharacterized. Here we show that histone deacetylase (HDAC) activity is required for the early stages of tail regeneration. HDAC1 is expressed during the 1st two days of regeneration. Pharmacological blockade of HDACs using Trichostatin A (TSA) increased histone acetylation levels in the amputated tail. Furthermore, treatment with TSA or another HDAC inhibitor, valproic acid, specifically inhibited regeneration. Over-expression of wild-type Mad3, a transcriptional repressor known to associate in a complex with HDACs via Sin3, inhibited regeneration. Similarly, expression of a Mad3 mutant lacking the Sin3-interacting domain that is required for HDAC binding also blocks regeneration, suggesting that HDAC and Mad3 may act together to regulate regeneration. Inhibition of HDAC function resulted in aberrant expression of Notch1 and BMP2, two genes known to be required for tail regeneration. Our results identify a novel early role for HDAC in appendage regeneration and suggest that modulation of histone acetylation is important in regenerative repair of complex appendages.
An Environmental Approach to Positive Emotion: Flowers

For more than 5000 years, people have cultivated flowers although there is no known reward for this costly behavior. In three different studies we show that flowers are a powerful positive emotion “inducer”. In Study 1, flowers, upon presentation to women, always elicited the Duchenne or true smile. Women who received flowers reported more positive moods 3 days later. In Study 2, a flower given to men or women in an elevator elicited more positive social behavior than other stimuli. In Study 3, flowers presented to elderly participants (55+ age) elicited positive mood reports and improved episodic memory. Flowers have immediate and long-term effects on emotional reactions, mood, social behaviors and even memory for both males and females. There is little existing theory in any discipline that explains these findings. We suggest that cultivated flowers are rewarding because they have evolved to rapidly induce positive emotion in humans, just as other plants have evolved to induce varying behavioral responses in a wide variety of species leading to the dispersal or propagation of the plants.
Differential gene expression analysis of Paracoccidioides brasiliensis during keratinocyte infection.

Paracoccidioides brasiliensis is the agent of paracoccidioidomycosis, one of the most important systemic fungal diseases in Latin America. This initiates in lung tissue and can subsequently disseminate to other tissues. Clinical manifestations range from localized forms to disseminated disease that can progress to lethality, probably depending on the relationships among the virulence of the fungus, the immune response and the ability to interact with the surface structures and invade epithelial cells and mononuclear cells of the host. It is generally regarded as a multifocal disease, with oral lesions as the prominent feature. The aim of this study was to evaluate P. brasiliensis yeast infection in normal oral keratinocytes (NOKs). The differential expression of mRNAs and proteins was also determined when the fungus was placed in contact with the cell in order to characterize differentially expressed genes and proteins during P. brasiliensis infection. After contact with NOKs, the fungus appeared to induce alterations in the cells, which showed cellular extensions and cavitations, probably resulting from changes in the actin cytoskeleton seen at 5 and 8 h after infection. Levels of protein expression were higher after reisolation of the fungus from infected NOK culture compared with culture of the fungus in medium. The analysis identified transcripts related to 19 proteins involved in different biological processes. Transcripts were found with multiple functions including induction of cytokines, protein metabolism, alternative carbon metabolism, zinc transport and the stress response during contact with NOKs. The proteins found suggested that the yeast was in a stress situation, as indicated by the presence of RDS1. Nevertheless, the yeast seemed to be proliferating and metabolically active, as shown by the presence of a proteasome, short-chain acetylator, glucosamine-6-phosphate isomerase and ADP/ATP carrier transcripts. Additionally, metabolic pathways may have been activated in order to eliminate toxic substances from the cell as a zinc transporter was detected, which is a potential target for the development of future drugs.
Implicit Messages: A Review of "Bias in Mental Testing"

A review of Jensen's impressive volume, Bias in Mental Testing, could either address the issues of bias that he considers, and thereby detail the virtues of this scholarly tome, or it could speak to the ghosts that haunt it. Because other reviewers in this series are likely to describe the major theses and lines of evidence in the book, I have chosen to confront the demonic implications in a rather brief ceremony. As a preface, let me say that I agree with Jensen's review of the literature on test construction, and I accept his major conclusions: that tests are not biased against blacks by the standards of test construction and validation, that the differences in performance between blacks and whites are really there, and that test differences have important implications for educational and occupational selection. If the racial differences in general ability are real and cannot be accounted for by biases in the tests, then what can be done about inequities in the distribution of social rewards? Not much, according to Jensen; the evidence for genetic differences in intelligence overwhelms any evidence for environmental effects, so that the reader is left with real differences, important consequences, and no remedies. Jensen's most important conclusions are never stated. By addressing so narrowly the scientific issues of test bias, Jensen has avoided an explicit statement of the conclusions that scream out from his pages: that blacks as a group will not succeed educationally and occupationally in this society, and their lack of success can be justified by their poor performance on tests that predict educational and occupational success. And there is the final, damning implication that the cause of their failures is the pervasive genetic difference in intelligence between the races. The apparition of racial genetic inferiority rises from this book. I will deal first with the ghost of racial genetic differences and then try a little exorcism through incantations about cultural differences in child rearing.
A Comparative Analysis of Changing Job Selection Attitudes and Expectations of Hospitality Students in Hong Kong and Mainland China

The purpose of the study was to explore hotel students perceived importance of job selection attributes and career expectations and perceptions before and after internship in Hong Kong and Mainland China. A questionnaire survey was conducted with 262 senior students at one university in Hong Kong and two universities in China. It was found that Hong Kong students intended to look for opportunities to learn new things while students from Mainland China focused on developing their skills and abilities. Before internship, both Hong Kong and Mainland Chinese students looked for pleasant people to work with and good possibilities for promotion and growth when selecting the job. After internship, Hong Kong students put more emphasis on good prospects for promotion while Mainland Chinese students tended to look for good remuneration.