Miracle-dz/UniFAR-FTUs huggingface dataset:
No evidence for accumulation of deleterious mutations and fitness degradation in clonal fish hybrids: Abandoning sex without regrets

Despite its inherent costs, sexual reproduction is ubiquitous in nature, and the mechanisms to protect it from a competitive displacement by asexuality remain unclear. Popular mutation‐based explanations, like the Muller's ratchet and the Kondrashov's hatchet, assume that purifying selection may not halt the accumulation of deleterious mutations in the nonrecombining genomes, ultimately leading to their degeneration. However, empirical evidence is scarce and it remains particularly unclear whether mutational degradation proceeds fast enough to ensure the decay of clonal organisms and to prevent them from outcompeting their sexual counterparts. To test this hypothesis, we jointly analysed the exome sequences and the fitness‐related phenotypic traits of the sexually reproducing fish species and their clonal hybrids, whose evolutionary ages ranged from F1 generations to 300 ky. As expected, mutations tended to accumulate in the clonal genomes in a time‐dependent manner. However, contrary to the predictions, we found no trend towards increased nonsynonymity of mutations acquired by clones, nor higher radicality of their amino acid substitutions. Moreover, there was no evidence for fitness degeneration in the old clones compared with that in the younger ones. In summary, although an efficacy of purifying selection may still be reduced in the asexual genomes, our data indicate that its efficiency is not drastically decreased. Even the oldest investigated clone was found to be too young to suffer fitness consequences from a mutation accumulation. This suggests that mechanisms other than mutation accumulation may be needed to explain the competitive advantage of sex in the short term.
Confined molecules: experiment meets theory in small spaces

Abstract The behavior of molecules confined to small spaces is fascinating chemistry and lies at the heart of signaling processes in biology. Our approach to confinement is through reversible encapsulation of small molecules in synthetic containers. We show that confinement leads to amplified reactivities in bimolecular reactions, stabilization of otherwise reactive species, and limitation in motions that create new stereochemical arrangements. The isolation of molecules from solvent makes for manageable computations and has stimulated theorist to examine reaction details in the limited space. Transition states for reactions and rearrangements can be calculated, the effects of (de)solvation can be evaluated and the magnetic properties of the containers can be compared with experimental observations. Finally, we outline several potential applications, including entanglement chemistry and the use of isomers in data storage.
Systemic acanthamoebiasis associated with canine distemper in dogs in the semiarid region of Paraíba , Brazil 1

Frade M.T. S. , Melo L.F. , Pessoa C.R. M. , Araújo J.L. , Fighera R.A. , Souza A.P., Uzal F. & Dantas A.F. M. 2015. Systemic acanthamoebiasis associated with canine distemper in dogs in the semiarid region of Paraíba, Brazil. Pesquisa Veterinária Brasileira 35(2):160-164. Hospital Veterinário, Laboratório de Patologia Animal, CSTR, Universidade Federal de Campina Grande, Campus de Patos, Av. Universitária s/n, Bairro Santa Cecília, Patos, PB 58708-110, Brazil. E-mail: dantas.af@uol.com. br Infections by free-living amoebae can cause systemic disease in animals and humans. We describe the epidemiological, clinical and pathological aspects of disseminated acanthamoebiasis associated with canine distemper in three dogs of the semiarid region of Paraíba, Northeastern Brazil. Affected dogs developed progressive neurological and respiratory signs that progressed to death within in two to 20 days. Gross lesions were irregular and with yellow-reddish nodules randomly distributed in the lungs, heart, kidneys, spleen, lymph nodes, adrenals, and intestine. One dog had foci of malacia in the parietal cortex and another one in nucleus of brain basis. Histologically, pyogranulomas with areas of necrosis and hemorrhage in all organs affected were observed, associated with myriads of intralesional amoebic trophozoites. All three cases were concomitant canine distemper, that possibly triggered immunosuppression in the dogs. The diagnosis was performed through microscopic findings of infection by free-living amoebae and confirmed Acanthamoeba sp. by immunohistochemistry.
Regulation of Hyaluronan Synthesis by UDP-sugars

Hyaluronan is a large glycosaminoglycan composed of alter­ nating units of N­acetylglucosamine (GlcNAc) and glucuronic acid (GlcUA). Hyaluronan is synthesized by hyaluronan syn­ thase enzymes (HAS1,2,3). In many tissues hyaluronan is a major component of the extracellular matrix. It enhances cell proliferation and migration, and controls differentia­ tion. High levels of hyaluronan are associated with cancer progression and inflammation. In this study a new inhibitor of hyaluronan synthesis, mannose, was discovered and it was demonstrated that this depletes UDP­GlcNAc content. The three HAS enzymes showed different sensitivities to the cel­ lular content of UDP­GlcNAc. HAS3 had the highest affinity with the precursors and HAS1 the lowest, suggesting that the HAS­isoenzyme distribution in a particular cell type deter­ mines the sensitivity of its hyaluronan synthesis to UDP­sugar supply. Interestingly, a feedback mechanism from UDP­sugar content to HAS2 expression was found, since fluctuations in UDP­GlcNAc content caused reciprocal changes in HAS2 tran­ scription. This regulation is probably mediated by O­GlcNAc modifications of transcription factors YY1 and SP1. This study also showed that hyaluronan­dependent binding of leukocytes can be induced by inflammatory mediators and cell stress, and inhibited by mannose. In an in vivo wound model mannose reduced hyaluronan level, granulation tissue growth and ac­ cumulation of leukocytes. Altogether, this work showed that cellular UDP­sugar content regulates hyaluronan synthesis and hyaluronan­mediated functions, such as cell migration, proliferation, and leukocyte adhesion. Therefore, inhibition of hyaluronan synthesis by a reduction in UDP­GlcNAc, us­ ing mannose or similar effectors, may provide novel ways to treat pathological processes that involve excessive hyaluronan production, e.g. inflammation and cancer.
A Systematic Literature Review of Personality Trait Classification from Textual Content

Abstract The day-to-day use of digital devices with Internet access, such as tablets and smartphones, has increased exponentially in recent years and this has had a consequent effect on the usage of the Internet and social media networks. When using social networks, people share personal data that is broadcast between users, which provides useful information for organizations. This means that characterizing users through their social media activity is an emerging research area in the field of Natural Language Processing (NLP) and this paper will present a review of how personality can be detected using online content. Approach A systematic literature review identified 30 papers published between 2007 and 2019, while particular inclusion and exclusion criteria were used to select the most relevant articles. Outcomes This review describes a variety of challenges and trends, as well as providing ideas for the direction of future research. In addition, personality trait identification and techniques were classified into different types, including deep learning, machine learning (ML) and semi-supervised/hybrid. Implications This paper’s outcomes will not only facilitate insight into the various personality types and models but will also provide knowledge about the relevant detection techniques. Novelty While prior studies have conducted literature reviews in the personality trait detection field, the systematic literature review in this paper provides specific answers to the proposed research questions. This is novel to this field as this particular type of study has not been conducted before.
Control of superficial scald of apples by low-oxygen atmospheres

HORTSCIENCE, VOL. 34(7), DECEMBER 1999 Received for publication 24 Feb. 1999. Accepted for publication 22 Apr. 1999. The cost of publishing this paper was defrayed in part by the payment of page charges. Under postal regulations, this paper therefore must be hereby marked advertisement solely to indicate this fact. Phone: 517-355-3286; fax: 517-381-0890; e-mail: dilley@pilot.msu. edu Control of Superficial Scald of Apples by Low-oxygen Atmospheres
On the correlation between allocation to defence and regrowth in plants

Because storage of resources to regrow after damage and investment in defence draw upon the same resource pool, it has been argued that they should show a negative correlation. We sketch a model for optimal allocation to defence and to storage for regrowth. In the model generalist herbivores exert a constant herbivore pressure against which the plant can defend itself. With discrete intervals, disturbance occurs by an external cause against which the plant cannot defend. This could be an abiotic disturbance or the outbreak of a specialist herbivore that is unaffected by the defence. If we compare genotypes or species, each adapted to its own habitat, then a positive correlation or no correlation between allocation to defence and to regrowth is to be expected. The parameter space in which plants should both defend and store resources for regrowth is limited. Especially under favourable growing conditions, plants should only allocate to growth. We discuss some experimental measures of the regrowth capacity of plants in the context of our model and argue that these should be used with caution.
Influence of trans-polyoctylene rubber content on styrene-butadiene rubber properties

Abstract The study was focused on the investigation of trans-polyoctylene (TOR) influence on cross-linking as well as mechanical and rheological properties of rubber compounds based on styrene-butadiene rubber (SBR). SBR was compounded with different proportions of TOR in the concentration range from 0 to 30 phr. Integration of TOR into rubber leads to the prolongation of the optimum curing time and scorch time and thus the decrease of the curing rate. Higher content of TOR led to less viscous rubber due to the plasticizing effect. Cross-link density of vulcanizates was reduced, which correlates with higher elongation at break. Tensile strength and hardness of vulcanizates increased with the increasing TOR content, probably due to the increasing amount of the crystalline phase.
Apple Orchard Productivity and Fruit Quality under Organic, Conventional, and Integrated Management

Located on a 20-ha commercial apple (Malus domestica Borkh.) orchard in the Yakima Valley, Washington, a 1.7-ha study area was planted with apple trees in 1994 in a randomized complete block design with four replications of three treatments: organic (ORG), conventional (CON), and integrated (INT). Soil classifi cation, rootstock, cultivar, plant age, and all other conditions except management were the same on all plots. In years 9 (2002) and 10 (2003) of this study, we compared the orchard productivity and fruit quality of 'Galaxy Gala' apples. Measurements of crop yield, yield effi ciency, crop load, average fruit weight, tree growth, color grades, and weight distributions of marketable fruit, percentages of unmarketable fruit, classifi cations of unmarketable fruit, as well as leaf, fruit, and soil mineral concentrations, were used to evaluate orchard productivity. Apple fruit quality was assessed at harvest and after refrigerated (0 to 1 °C) storage for three months in regular atmosphere (ambient oxygen levels) and for three and six months in controlled atmosphere (1.5% to 2% oxygen). Fruit internal ethylene concentrations and evolution, fruit respiration, fl esh fi rmness, soluble solids concentration (SSC), titratable acidity (TA), purgeable volatile production, sensory panels, and total antioxidant activity (TAA) were used to evaluate fruit quality. ORG crop yields were two-thirds of the CON and about half of the INT yields in 2002, but about one-third greater than either system in 2003. High ORG yields in 2003 resulted in smaller ORG fruit. Inconsistent ORG yields were probably the result of several factors, including unsatisfactory crop load manage- ment, higher pest and weed pressures, lower leaf and fruit tissue nitrogen, and defi cient leaf tissue zinc concentrations. Despite production diffi culties, ORG apples had 6 to 10 N higher fl esh fi rmness than CON, and 4 to 7 N higher than INT apples, for similar-sized fruit. Consumer panels tended to rate ORG and INT apples to have equal or better over- all acceptability, fi rmness, and texture than CON apples. Neither laboratory measure- ments nor sensory evaluations detected differences in SSC, TA, or the SSC to TA ratio. Consumers were unable to discern the higher concentrations of fl avor volatiles found in CON apples. For a 200 g fruit, ORG apples contained 10% to 15% more TAA than CON apples and 8% to 25% more TAA than INT apples. Across most parameters measured in this study, the CON and INT farm management systems were more similar to each other than either was to the ORG system. The production challenges associated with low-input organic apple farming systems are discussed. Despite limited technologies and products for organic apple production, the ORG apples in our study showed improvements in some fruit quality attributes that could aid their marketability.
New models and algorithms for RNA pseudoknot order assignment

Abstract The pseudoknot is a specific motif of the RNA structure that highly influences the overall shape and stability of a molecule. It occurs when nucleotides of two disjoint single-stranded fragments of the same chain, separated by a helical fragment, interact with each other and form base pairs. Pseudoknots are characterized by great topological diversity, and their systematic description is still a challenge. In our previous work, we have introduced the pseudoknot order: a new coefficient representing the topological complexity of the pseudoknotted RNA structure. It is defined as the minimum number of base pair set decompositions, aimed to obtain the unknotted RNA structure. We have suggested how it can be useful in the interpretation and understanding of a hierarchy of RNA folding. However, it is not trivial to unambiguously identify pseudoknots and determine their orders in an RNA structure. Therefore, since the introduction of this coefficient, we have worked on the method to reliably assign pseudoknot orders in correspondence to the mechanisms that control the biological process leading to their formation in the molecule. Here, we introduce a novel graph coloring-based model for the problem of pseudoknot order assignment. We show a specialized heuristic operating on the proposed model and an alternative integer programming algorithm. The performance of both approaches is compared with that of state-of-the-art algorithms which so far have been most efficient in solving the problem in question. We summarize the results of computational experiments that evaluate our new methods in terms of classification quality on a representative data set originating from the non-redundant RNA 3D structure repository.
PISA Performance of Natives and Immigrants: Selection versus Efficiency

Abstract In most countries, immigrant and native students perform differently in the Programme for International Student Assessment (PISA) due to two main reasons: different immigration regimes and differences in their home-country educational systems. While there is sophisticated literature on the reasons for these performance gaps, it is barely considered in the educational efficiency research. Our approach distinguishes between selection effects caused by immigration policies, and the efficiency of educational systems in integrating immigrant students, given their socio–economic background. Accordingly, we split our sample, which consists of 153,374 students in 20 countries, calculate various different efficient frontiers, and ultimately decompose and interpret the resulting efficiency values. We find large differences in educational system efficiency, when controlling for negative selection effects caused by immigration regimes.
Brain control of appetite during sickness

Given the high‐energy requirements to sustain immune responses and healing processes, it is intriguing that lack of appetite (i.e., anorexia) is a cardinal feature of sickness behaviour. While our understanding of the brain mechanisms that control appetite is rapidly growing, how inflammation affects these mechanisms is not fully understood. Here, we discuss advances in our understanding of discrete appetite controlling mechanisms and how inflammation influences their function. We further discuss the pathophysiological significance of anorexia and negative energy balance during the immune regulatory response.
Influence of Density and Climate on Population Dynamics of a Large Herbivore Under Harsh Environmental Conditions

Abstract Dynamics of herbivore populations can be influenced both by density-dependent processes and climate. We used age-at-harvest data for adult female white-tailed deer (Odocoileus virginianus) collected over 23 years to estimate survival and reproduction by age class and to identify effects of environmental factors. The study population was located on Anticosti Island (QC, Canada), at the northern limit of the species' range; the population was at high density, and the landscape had scarce forage and abundant snow during winter. Despite severe environmental conditions, population growth apparently increased during the study; adult survival was similar to other populations, although reproduction appeared lower. Winter severity was not related to survival, but density affected adult female survival. Density at estrus was the main factor influencing reproduction of 2- and 3–4-year-olds and also affected reproduction of prime-aged females (5–9-yr-olds), but not of older females. Reproductive rate of younger females was influenced by environmental conditions in autumn, such as high density or snow conditions that limited forage availability. Reproductive success of 5–9- and ≥10-year-old females appeared dependent on spring conditions favoring high-quality forage, probably through effects on neonatal survival. Relative to other studies on northern ungulates, demographic processes in our study appeared to be more affected by autumn and spring climate, in addition to population density, than by winter climate. We thus propose that population density, as well as autumn and spring climate, should be considered in management strategies. Harvest data offered a unique opportunity to study forest ungulates, for which individual monitoring is rarely possible.
How Effective is Personalization in Persuasive Interventions for Reducing Sedentary Behavior and Promoting Physical Activity: A Systematic Review

The use of persuasive systems and devices to reduce sedentary lifestyles and encourage individuals to be more physically active is progressively gaining interest. This paper presents a 13 years review (from 2006 to 2019) of personalized persuasive technologies (PTs) for promoting physical activity (PA) and discouraging sedentary behavior (SB) . Moreover, we decon-structed the various implementations and operationalizations of the personalization in these PTs and compared their effectiveness. Specifically, this paper aims to (1) shed light on the multiple ways of implementing personalization in these PTs to promote PA and reducing SB, (2) evaluate the effectiveness of personalized PTs for promoting PA and decreasing SB, (3) highlight trends and offer suggestions for research in the area of personalizing PTs.
THE EFFECT OF DIFFERENT GROWTH MEDIA, CARBON SOURCE AND PGRs ON DENDROBIUM BROGA GIANT ORCHID'S PROTOCORM-LIKE BODIES (PLBs) PROLIFERATION SUPPORTED WITH SEM AND TEM ANALYSIS

DendrobiumBrogaGiant�( Dendrobium BobbyMessina�×� DendrobiumSuperbiens)�isaneworchidhybridinMalaysia. � Theaimofthisstudywastoinvestigatetheeffect �ofdifferentgrowthmedia,�carbonsourcesandPGRs �onDendrobium BrogaGiantorchid'sprotocorm$likebodies�(PLBs)�p roliferationsupportedwithSEMandTEManalysis. �T hePLBswere� culturedondifferentstrengthofsemi$solidandli quidMSmediumandtheproliferationratewasrecor dedbasedonthefresh� weightbasis. �ThemaximumPLBsproliferation�(12.31 %�±�0.57)�wasobtainedin�½�MSsemi$solidmedium. �P LBswere� culturedon�½�MSsemi$solidmediasupplementedwith �differentsucroseconcentrations�(0,�10,�20,�30�&� 40�g.L $1 ). �The� highestproliferationrateofPLBs�(15.48%�±�1.20)� wasrecordedfrom�½�MSsupplementedwith�20�g.L $1 �sucrose. �Different� concentrationsofBAP�(0,�0.5,�1.0,�2.0�mg.L $1 )�andNAA�(0,�0.5,�1.0,�2.0�mgL $1 )�wereaddedto�½�MSsemi$solidmedium. � Combinationsof�1.0�mg.L $1 �BAPand�0.5�mg.L $1 �NAAproducedhigherPLBsproliferation. �Micromorph ologicalstudiesby� SEMandTEMdisplayedtrichome,�leafprimordial,�st omata,�varioussizesofmitochondria,�vacuoles,�dif ferentshapesof� chloroplastwerefoundinPLBswhichamelioratedth eslowproliferationnatureofplantlets. �
Starting points for small mammal population recovery after wildfire: recolonisation or residual populations?

Wildfire is a major driver of spatio-temporal variation in terrestrial ecosystems. Large wildfires are predicted to occur more frequently due to climate change. The mechanisms by which post-fire recovery proceeds are influenced by the abundance of survivors, and their distribution in relation to habitat variability and refugia. Thus, characterising early post-fire demographic processes is critical to understanding the demographic and community-level responses of ecosystems to fire. The Black Saturday fires of February 2009 burnt an area of approximately 3500 km2 in Victoria, Australia. We quantified the effects of this high severity forest fire on the habitat, abundance, sex ratio and body mass of two small mammal species, the agile antechinus Antechinus agilis and bush rat Rattus fuscipes. We developed a hypothetical framework to distinguish in situ survival and rapid recolonisation as the processes underlying short-term post-fire distributions. These hypotheses were based on expected patterns of abundance over increasing distances from unburnt sources, and the estimated recolonisation capabilities of each species and sex. The agile antechinus and bush rat were present in burnt sites at 30% and 12% of the density observed in unburnt sites. In situ survival, and not recolonisation, was the most plausible explanation for our findings. Abundance and body mass data indicated a greater effect of fire on the bush rat than the agile antechinus. The bush rat showed a shift in topographic association, whereby drainage lines acted as post-fire refugia. Our findings suggest these species do not depend on recolonisation for recovery, and that the bush rat will follow a nucleated recovery, expanding from topographic refugia. Thus, connectivity-reducing management activities, such as salvage logging and firebreak and road construction, may not affect the early stages of population recovery in remaining stands of burnt forest. Rather, ongoing recovery is likely to be limited by demographic rates and resource availability.