Miracle-dz/UniFAR-FTUs huggingface dataset:
Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes

Intergenerational Transposable Shutdown Transposable elements (TEs) are a potential threat, especially to the germline genome. In many eukaryotes, TEs are shut down by DNA methylation and/or small-RNA–mediated silencing. Therefore, it seems counterintuitive that results obtained by Ibarra et al. (p. 1360) on Arabidopsis showed that in the cells of this plant's sexual apparatus, many small TEs are demethylated by DEMETER (DME) DNA glycosylase and become activated. But it turns out that activation of the TEs triggers the formation of small-interfering RNAs, which in these experiments were seen to travel from the surrounding cells to the egg. Thus, activation of TEs in the companion cells “immunizes” the gametes via the interfering RNAs that shutdown the TEs in the gametes permanently. Activation of transposable elements in the companion cells of plant gametes can silence transposable elements in the gamete. The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes DNA demethylation before fertilization, but the targeting preferences, mechanism, and biological significance of this process remain unclear. Here, we show that active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for all of the demethylation in the central cell and preferentially targets small, AT-rich, and nucleosome-depleted euchromatic transposable elements. The vegetative cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation of similar sequences, and lack of DEMETER in vegetative cells causes reduced small RNA–directed DNA methylation of transposons in sperm. Our results demonstrate that demethylation in companion cells reinforces transposon methylation in plant gametes and likely contributes to stable silencing of transposable elements across generations.
Porphyry-Copper Ore Shells Form at Stable Pressure-Temperature Fronts Within Dynamic Fluid Plumes

Earning a High Grade Most of the world's copper and molybdenum come from porphyry-type ore deposits in Earth's crust. The metals are deposited either as veins of concentrated metals in fractured rock or in a confined shell, associated with the edges of magma chamber plumes. But it remains unclear why a front of sharp temperature-pressure gradients, which allows the accumulation of high-grade metal deposits, remains stable. Weis et al. (p. 1613, published online 15 November; see the Perspective by Ingebritsen) constructed a hydrothermal model of a porphyry-type system given a supply of magmatic fluids with high metal concentrations. The thermodynamic properties of injected volatile fluids and dynamic variations in host rock permeability, driven by injection-induced fracturing, controlled the stability and evolution of the fronts and allowed for the formation of an extensive network of ore veins from within the magmatic chamber. A numerical model attributes ore metal accumulation in porphyry deposits to fluid plumes draining from large magma chambers. Porphyry-type ore deposits are major resources of copper and gold, precipitated from fluids expelled by crustal magma chambers. The metals are typically concentrated in confined ore shells within vertically extensive vein networks, formed through hydraulic fracturing of rock by ascending fluids. Numerical modeling shows that dynamic permeability responses to magmatic fluid expulsion can stabilize a front of metal precipitation at the boundary between lithostatically pressured up-flow of hot magmatic fluids and hydrostatically pressured convection of cooler meteoric fluids. The balance between focused heat advection and lateral cooling controls the most important economic characteristics, including size, shape, and ore grade. This self-sustaining process may extend to epithermal gold deposits, venting at active volcanoes, and regions with the potential for geothermal energy production.
Role of aqueous Bryoria capillaris (Ach.) extract as a genoprotective agent on imazalil-induced genotoxicity in vitro

In recent years, a number of studies have suggested that lichens might be the easily accessible sources of natural drugs that could be used as a possible food supplement. Extensive research is being carried out to explore the importance of lichen species, which are known to contain a variety of pharmacological active compounds. On the other hand, imazalil (IMA), a commonly used fungicide in both agricultural and clinical domains, is suspected to produce very serious toxic effects in vertebrates. In this context, the antigenotoxic effect of aqueous Bryoria capillaris (Ach.) extract (BCE) was studied against the genotoxic damage induced by IMA on cultured human lymphocytes using chromosomal aberrations (CA) and micronucleus (MN) as cytogenetic parameters. Human peripheral lymphocytes were treated in vitro with varying concentrations of BCE (5, 10, 25, 50 and 100 µg/mL), tested in combination with IMA (336 µg/mL). BCE alone was not genotoxic, and when combined with IMA treatment, it reduced the frequency of CAs and the rates of MN. A clear dose-dependent decrease in the genotoxic damage of IMA was observed, suggesting a genoprotective role of BCE. The results of the present study suggest that this plant extract per se do not have genotoxic potential, but can modulate the genotoxicity of IMA on peripheral human lymphocytes in vitro. In conclusion, our findings may have an important application in the protection of cultured human lymphocyte from the genetic damage and side effects induced by agricultural and medical chemicals that are hazardous to people.
Determination of cytotoxic and genotoxic effects of naphthalene, 1-naphthol and 2-naphthol on human lymphocyte culture

Naphthalene, a bicyclic aromatic hydrocarbon, has toxic effects on animals and humans. Although recent studies stressed on the genotoxic and cytotoxic effects of naphthalene and its metabolites on eukaryotic cells, there is a big controversy among the results of these studies. The aim of this study is to investigate the effects of naphthalene and its metabolites on the cytotoxicity and genotoxicity in the human lymphocytes in the culture. The genotoxic and cytotoxic effects of naphthalene and its metabolites, 1-naphthol and 2-naphthol, were studied using cytotoxicity test (lactate dehydrogenase and cell proliferation (WST-1) assays) and DNA fragmentation assay (terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay). Naphthalene and its metabolites had no significant cytotoxic effect on treated samples when compared with untreated ones. This result was also confirmed by WST-1 assay. In the TUNEL assay, DNA fragmentation was induced significantly by all concentrations of naphthalene and 2-naphthol and 50 and 100 µM concentrations of 1-naphthol (p < 0.05 or 0.001). In the DNA fragmentation, the most effective dose of 2-naphthol (63%) was 100 µM, when compared with negative control group (13%). These results suggest that naphthalene and its metabolites, 1-naphthol and 2-naphthol, may cause DNA damage on human lymphocytes.
Prescriptions, licences and evidence

Aims and method There is considerable confusion at present among clinicians as regards the appropriateness of prescribing off-licence. Because of the nature of the registration process it is likely that a considerable proportion of prescribing will always be off-licence. This paper seeks to clarify when it is appropriate to prescribe off-licence. We convened a workshop on behalf of the British Association for Psychopharmacology involving clinicians and regulators from a variety of countries to explore this issue both generally and for specific childhood and learning disability clinical situations. Recent statements from the defence unions and consumer groups were also scrutinised. Results Across senior clinicians and regulators from a number of European countries and North America, there is a consensus that prescribing off-licence is a necessary part of the art of medicine. Clinical implications Current advice to clinicians on the issue of off-licence prescribing can sometimes overemphasise the hazards and neglect the benefits that may stem from appropriate off-licence prescribing. Good prescribing involves specifying treatment goals and monitoring outcomes and it is more important to share this with the patient than it is to communicate the licensed status of the drug being prescribed.
Effect of selenium on methimazole-induced liver damage and oxidative stress in adult rats and their offspring

This study aimed to investigate the protective effect of selenium (Se) on methimazole (MMI; an antithyroid drug)-induced hepatotoxicity in adult rats and their progeny. Female Wistar rats were randomly divided into four groups of six rats in each group: group I served as controls that received standard diet; group II received MMI in drinking water as 250 mg L−1 and standard diet; group III received both MMI (250 mg L−1, orally) and Se (0.5 mg kg−1 of diet); group IV received Se (0.5 mg kg−1 of diet) as sodium selenite. Treatments were started from the 14th day of pregnancy until day 14 after delivery. Exposure of rats to MMI promoted oxidative stress with an increase in liver malondialdehyde levels, advanced oxidation protein products and protein carbonyl contents and a decrease in the levels of glutathione, nonprotein thiols and vitamin C. A decrease in the activities of liver glutathione peroxidase, superoxide dismutase, catalase and lactate dehydrogenase and in the levels of plasma total protein and albumin was also observed. Plasma transaminase activities and total, direct and indirect bilirubin levels increased. Coadministration of Se through diet improved all biochemical parameters. The histopathological changes confirmed the biochemical results. Therefore, our investigation revealed that Se, a trace element with antioxidant properties, was effective in preventing MMI-induced liver damage.
Anterior Cruciate Ligament Healing and Repair

The anterior cruciate ligament (ACL) fails to heal adequately after rupture, even after partial injuries or primary repair. This is vastly different from the extra-articular medial collateral ligament (MCL), which heals even without surgical intervention. The reasons for this involve cellular and structural factors. On a cellular level, ACL cells have decreased migration and different extracelluar matrix production profiles when compared with MCL cells; however, it is unlikely that these small differences are fully responsible for the stark dichotomy in healing response for the two ligaments. With regards to structural issues, recent experiments have shown a premature loss of the bridge between the ruptured ACL ends, and this structural defect is also likely a key factor in the failure of the ACL to heal. New approaches using a substitute bridge, or provisional scaffold, with implanted growth factors are being developed to stimulate the ACL to heal after primary repair. To lay the foundation for these new approaches, the four phases of the injury response in the ACL (inflammatory, epiligamentous regeneration, proliferative, and remodeling phases), and the differences in intrinsic ACL and MCL cellular response are reviewed in this article followed by a discussion of the manipulations currently being attempted to improve the healing response of the ACL, including hyaluronic acid, implanted growth factors, and tissue engineered scaffolds.
Diffusion of innovations in social networks

While social networks do affect diffusion of innovations, the exact nature of these effects are far from clear, and, in many cases, there exist conflicting hypotheses among researchers. In this paper, we focus on the linear threshold model where each individual requires exposure to (potentially) multiple sources of adoption in her neighborhood before adopting the innovation herself. In contrast with the conclusions in the literature, our bounds suggest that innovations might spread further across networks with a smaller degree of clustering. We provide both analytical evidence and simulations for our claims. Finally, we propose an extension for the linear threshold model to better capture the notion of path dependence, i.e., a few minor shocks along the way could alter the course of diffusion significantly.
Small bowel transplantation: a work in progress

Purpose of reviewThe complexities of small bowel transplantation have made its successful clinical application a significant challenge. Many strategies that have been highly successful in improving the outcomes of other types of transplantations have had limited success with small bowel transplantations. Despite this, the results have slowly been improving, primarily because of better overall clinical acumen based on a better understanding of the unique complexities of small bowel transplantation. This has evolved primarily as a result of ongoing clinical observation with resultant modifications in clinical management practices. Recent findingsAlthough basic science research efforts played a limited role in the early clinical development of small bowel transplantation, they are becoming increasingly important in defining the unique immunologic, physiologic, and microbiologic problems that limit further progress. SummaryThis review summarizes some of the major issues that make small bowel transplantation unique and challenging and the clinical and basic science research that has been done in an attempt to clarify and resolve these issues.
Natural Enemies Drive Geographic Variation in Plant Defenses

Plant Anti-Insect Armaments Because individual plants are unable to relocate, they are subject to extreme selection by the insects feeding upon them. One means by which plants suppress herbivory is to produce toxic compounds to deter feeding (see the Perspective by Hare). Agrawal et al. (p. 113) compared pesticide–treated or untreated evening primroses. Over 5 years of pesticide treatment, the production of defensive chemicals in the fruit reduced and flowering times shifted, and the primrose's competitive ability against dandelions improved. Züst et al. (p. 116) examined large-scale geographic patterns in a polymorphic chemical defense locus in the model plant Arabidopsis thaliana and found that it is matched by changes in the relative abundance of two specialist aphids. Thus, herbivory has strong and immediate effects on the local genotypic composition of plants and traits associated with herbivore resistance. A field study demonstrates that specialist aphid feeders cause changes in the defenses mounted by plants. Plants defend themselves against attack by natural enemies, and these defenses vary widely across populations. However, whether communities of natural enemies are a sufficiently potent force to maintain polymorphisms in defensive traits is largely unknown. Here, we exploit the genetic resources of Arabidopsis thaliana, coupled with 39 years of field data on aphid abundance, to (i) demonstrate that geographic patterns in a polymorphic defense locus (GS-ELONG) are strongly correlated with changes in the relative abundance of two specialist aphids; and (ii) demonstrate differential selection by the two aphids on GS-ELONG, using a multigeneration selection experiment. We thereby show a causal link between variation in abundance of the two specialist aphids and the geographic pattern at GS-ELONG, which highlights the potency of natural enemies as selective forces.
Getting to the Root of Aging

Why do patterns of aging differ widely across the tree of life? As people live longer, the question arises of how malleable aging is and whether it can be slowed or postponed. The classic evolutionary theories of aging (1—4) provide the theoretical framework that has guided aging research for 60 years. Are the theories consistent with recent evidence?
Formation of Regular Satellites from Ancient Massive Rings in the Solar System

An analytical model suggests that the terrestrial and giant planets in the solar system formed moons through a similar process. When a planetary tidal disk—like Saturn’s rings—spreads beyond the Roche radius (inside which planetary tides prevent aggregation), satellites form and migrate away. Here, we show that most regular satellites in the solar system probably formed in this way. According to our analytical model, when the spreading is slow, a retinue of satellites appear with masses increasing with distance to the Roche radius, in excellent agreement with Saturn’s, Uranus’, and Neptune’s satellite systems. This suggests that Uranus and Neptune used to have massive rings that disappeared to give birth to most of their regular satellites. When the spreading is fast, only one large satellite forms, as was the case for Pluto and Earth. This conceptually bridges the gap between terrestrial and giant planet systems. There is a good understanding of how Jupiter's Galilean moons (Io, Europa, Ganymede, and Callisto) and Saturn's largest moon, Titan, formed, but the same is not true for the other regular moons of the giant planets. Crida and Charnoz (p. 1196) describe a model whereby most of the regular moons (those with little orbital inclination or eccentricity) in the solar system were born in ancient massive rings that surrounded their planets. This model does not apply to Jupiter, but it can explain the regular moons of the other giant planets, including Titan, and even those of Earth and Pluto. The model further predicts that Uranus and Neptune once had massive, Saturn-like rings, which gave birth to moons and then disappeared.
Earthquakes in the Lab

Friction experiments using a flywheel-based apparatus can be used to simulate natural earthquakes. Understanding how earthquakes of different sizes occur is one of the most challenging questions in fault and earthquake mechanics. On page 101 of this issue, Chang et al. (1) report the results of a carefully conducted experiment using a spinning flywheel attached to a high-velocity frictional testing machine to produce what they term an earthquake-like slip event. By changing the rate of revolution of the flywheel, the amount of kinetic energy transferred to the simulated fault in Sierra White granite or Kasota dolomite could be varied by about six orders of magnitude and could produce a series of frictional slips ranging from 0.003 to 4.6 m, corresponding to a moment magnitude range of Mw = 4 to 8 with respect to the range of fault displacements. The power relationship between energy input and displacement is similar to that found for natural earthquakes. Also, the slip produced by the flywheel is characterized by very rapid initial acceleration followed by gradual deceleration, somewhat similar to slip history recognized for natural earthquakes (2). Such experiments will arouse discussions about whether they are realistic proxies of natural earthquakes.
Walking on Solid Ground

A gel-on-brush model for the mucosal surfaces in the human airways helps to explain how common airway diseases arise. Mucosal surfaces throughout the human body—including those of the respiratory, gastrointestinal, and genitourinary tracts—are wet tissues that include some form of mucus gel among their defenses (1). In the airways, the mucus gel layer is propelled out of the lungs by ciliary beating and continually renewed by secretion of polymeric mucins (see the figure, panels A and B). This process enables the rapid removal of inhaled pathogens and toxicants (2). The conventional model has been that the mucus gel layer is suspended above a fluid periciliary layer by the beating of cilia. However, as Button et al. report on page 937 of this issue (3), this model is fundamentally wrong. The authors show that the periciliary layer has a macromolecular glycoconjugate structure with a higher density than the mobile gel layer. This dense network is grafted to the epithelial surface.
Pico-Newton order force measurement using a calibrated carbon nanotube probe by electromechanical resonance

Force measurement with pico-Newton (pN) order resolution using a carbon nanotube (CNT) probe, which is calibrated by the electromechanical resonance is presented. Based on the theoretical analysis, a CNT is suitable material for the sensitive force measurement. A CNT probe is constructed by attaching a CNT to the tip of the commercially available atomic force microscope (AFM) cantilever or tungsten needle probe by the electron-beam-induced deposition (EBID) though the nanorobotic manipulators inside a field-emission scanning electron microscope (FE-SEM). In order to attach a CNT quickly and correctly, CNTs are dispersed in ethanol by ultrasonic waves for several hours and oriented by electrophoresis. The elastic moduli of CNTs are calibrated from electromechanical resonance frequency by applied electrostatic forces. We measured pico-Newton order contact forces with a CNT probe, which is constructed with nanorobotic manipulators, by measuring deformation of a CNT probe from FE-SEM images.
Animal Behavior and the Microbiome

Feedbacks between microbiomes and their hosts affect a range of animal behaviors. Human bodies house trillions of symbiotic microorganisms. The genes in this human microbiome outnumber human genes by 100 to 1, and their study is providing profound insights into human health. But humans are not the only animals with microbiomes, and microbiomes do not just impact health. Recent research is revealing surprising roles for microbiomes in shaping behaviors across many animal taxa—shedding light on how behaviors from diet to social interactions affect the composition of host-associated microbial communities (1, 2), and how microbes in turn influence host behavior in dramatic ways (2–6).
When She is Gone: Child Care Plans of Mozambican Mothers with Terminal Illnesses

This study explored the child welfare plans of 102 mothers with terminal illnesses (predominantly AIDS) in rural Mozambique. The majority of mothers assumed that after their death the extended family would care for the children, but none offered a clearly identified plan. Many hoped that the government would provide for the children's education, food, and health care, although very little assistance is available currently. The vast majority of the women reported a preference for placement in an orphanage over other options, due to the perception that the children will be better fed and educated there. Ironically, all orphanages in Mozambique are at full capacity. The findings suggest an urgent need for collaboration at community, national, and international levels to meet the needs of orphans. Policy, practice, and research implications are explored.
Analysis of creeping locomotion of a snake robot on a slope

Biological snakes' diverse locomotion modes and physiology make them supremely adapted for environment. To realize these snakes' noticeable features, we have developed a snake-like robot that has no any forward direction driving force. To enlarge the environment-adaptable ability of our robot, in this study we discuss the creeping locomotion of our snake-like robot on a slope. A computer simulator is presented for analysis of the creeping locomotion of our snake-like robot on a slope, and the environment-adaptable body shape for the creeping locomotion of the snake-like robot on slope is also derived through this simulator.
How Information Theory Handles Cell Signaling and Uncertainty

Information theory allows analyses of cell signaling capabilities without necessarily requiring detailed knowledge of the signaling networks. Intracellular biochemical networks have traditionally been studied by stimulating populations of genetically identical cells and measuring the aggregate response. However, such population-based measurements may obscure the idiosyncrasies of individual cells and therefore suggest deceptively precise input-output relationships. Consequently, signaling pathways have been viewed as the finely tuned circuitry that programs the cell to behave in a predefined manner (1). Detailed studies of cellular biochemistry at the single-cell level now show that cells responding en masse may have quite varied behaviors when examined individually (2), raising the question of how precisely signaling pathways can control a cell's actions (3).