Miracle-dz/UniFAR-FTUs huggingface dataset:
Roots and Associated Fungi Drive Long-Term Carbon Sequestration in Boreal Forest

Forest Fungi Boreal forest is one of the world's major biomes, dominating the subarctic northern latitudes of Europe, Asia, and America. The soils of boreal forest function as a net sink in the global carbon cycle and, hitherto, it has been thought that organic matter in this sink primarily accumulates in the form of plant remains. Clemmensen et al. (p. 1615; see the Perspective by Treseder and Holden) now show that most of the stored carbon in boreal forested islands in Sweden is in fact derived from mycorrhizal mycelium rather than from plant litter. Biochemical and sequencing studies show that carbon sequestration is regulated by functional and phylogenetic shifts in the mycorrhizal fungal community. The results will need to be explicitly considered in models of the role of the boreal forest in the global carbon cycle. Reservoirs of carbon in boreal forest soils are revisited in an island chronosequence, using modeling and molecular approaches. [Also see Perspective by Treseder and Holden] Boreal forest soils function as a terrestrial net sink in the global carbon cycle. The prevailing dogma has focused on aboveground plant litter as a principal source of soil organic matter. Using 14C bomb-carbon modeling, we show that 50 to 70% of stored carbon in a chronosequence of boreal forested islands derives from roots and root-associated microorganisms. Fungal biomarkers indicate impaired degradation and preservation of fungal residues in late successional forests. Furthermore, 454 pyrosequencing of molecular barcodes, in conjunction with stable isotope analyses, highlights root-associated fungi as important regulators of ecosystem carbon dynamics. Our results suggest an alternative mechanism for the accumulation of organic matter in boreal forests during succession in the long-term absence of disturbance.
Exoplanet Habitability

The search for exoplanets includes the promise to eventually find and identify habitable worlds. The thousands of known exoplanets and planet candidates are extremely diverse in terms of their masses or sizes, orbits, and host star type. The diversity extends to new kinds of planets, which are very common yet have no solar system counterparts. Even with the requirement that a planet’s surface temperature must be compatible with liquid water (because all life on Earth requires liquid water), a new emerging view is that planets very different from Earth may have the right conditions for life. The broadened possibilities will increase the future chances of discovering an inhabited world.
Injectable, Cellular-Scale Optoelectronics with Applications for Wireless Optogenetics

The Smaller, the Better New semiconductor device technology enables injection of light-emitting diodes, silicon devices, actuators, and sensors at precisely controlled locations within biological tissues, such as the brain. Kim et al. (p. 211) show how wireless control of animal models using these technologies and the techniques of optogenetics provide new insights into basic behavioral neuroscience. Miniaturized and implantable light-emitting diodes offer precise and flexible control of neurons, when used in combination with optogenetics. Successful integration of advanced semiconductor devices with biological systems will accelerate basic scientific discoveries and their translation into clinical technologies. In neuroscience generally, and in optogenetics in particular, the ability to insert light sources, detectors, sensors, and other components into precise locations of the deep brain yields versatile and important capabilities. Here, we introduce an injectable class of cellular-scale optoelectronics that offers such features, with examples of unmatched operational modes in optogenetics, including completely wireless and programmed complex behavioral control over freely moving animals. The ability of these ultrathin, mechanically compliant, biocompatible devices to afford minimally invasive operation in the soft tissues of the mammalian brain foreshadow applications in other organ systems, with potential for broad utility in biomedical science and engineering.
Clinical anatomy of the peritoneal mesothelium: A review

This paper reviews the structure, function, and clinical significance of peritoneal mesothelium, once thought to be a passive membrane, but now known to play an active role in exchanges between the peritoneal cavity and the blood. The advent of continuous ambulatory peritoneal analysis (CAPD) has revived interest in the peritoneum, whose ultrastructure is much changed by CAPD.
Cell Death from Antibiotics Without the Involvement of Reactive Oxygen Species

Antibiotic Mechanisms Revisited Several recent studies have suggested that bactericidal antibiotics kill cells by a common mechanism involving reactive oxygen species (ROS). Two groups tested this hypothesis using diverse experiments, with both finding that quinolone, lactam, and aminoglycoside antibiotics had similar efficacy for killing in the presence or absence of oxygen (or nitrate). Liu et al. (p. 1210) saw no increase in hydrogen peroxide production in antibiotic-exposed cells and found no association between antibiotic exposure and the expected symptoms of oxidative damage, such as the breakdown of iron-sulfur clusters in enzymes or of hydroxyl radical injuries to DNA. Similarly, Keren et al. (p. 1213) found no correlation between the production of ROS, inferred from hydroxyphenyl fluorescein dye measurements, and bacterial survival, nor was there any significant protective effect engendered by thiourea. The results do not support a common mode of action for bactericidal antibiotics mediated by ROS. Tests of the oxidative damage mechanism for antibiotic killing do not support the generality of the hypothesis. Recent observations have suggested that classic antibiotics kill bacteria by stimulating the formation of reactive oxygen species (ROS). If true, this notion might guide new strategies to improve antibiotic efficacy. In this study, the model was directly tested. Contrary to the hypothesis, antibiotic treatment did not accelerate the formation of hydrogen peroxide in Escherichia coli and did not elevate intracellular free iron, an essential reactant for the production of lethal damage. Lethality persisted in the absence of oxygen, and DNA repair mutants were not hypersensitive, undermining the idea that toxicity arose from oxidative DNA lesions. We conclude that these antibiotic exposures did not produce ROS and that lethality more likely resulted from the direct inhibition of cell-wall assembly, protein synthesis, and DNA replication.
Cellular Self-Defense: How Cell-Autonomous Immunity Protects Against Pathogens

Defense and Counter-Defense Provided a pathogen can enter the body and survive coughing and spluttering, peristalsis, and mucus, the first active responses the host evokes to an invading organism will be at the level of the first cell encountered, well before classical cellular immunity and antibody responses are initiated. Randow et al. (p. 701) review the range of intracellular defenses against incoming pathogens and describe how compartmental boundaries within the cell provide multiple levels at which pathogens can be thwarted in their attempts to subjugate the cell to do their bidding. Baxt et al. (p. 697) review the range of evasion tactics that bacterial pathogens can summon to counter host repulsion and establish a niche in which to replicate and ensure onward transmission. Our prevailing view of vertebrate host defense is strongly shaped by the notion of a specialized set of immune cells as sole guardians of antimicrobial resistance. Yet this view greatly underestimates a capacity for most cell lineages—the majority of which fall outside the traditional province of the immune system—to defend themselves against infection. This ancient and ubiquitous form of host protection is termed cell-autonomous immunity and operates across all three domains of life. Here, we discuss the organizing principles that govern cellular self-defense and how intracellular compartmentalization has shaped its activities to provide effective protection against a wide variety of microbial pathogens.
Tactile sensing: Steps to artificial somatosensory maps

In this paper a framework for representing tactile information in robots is discussed. Control models exploiting tactile sensing are fundamental in social Human-Robot interaction tasks. Difficulties arising in rendering the sense of touch in robots are at different levels: both representation and computational issues must be considered. A layered system is proposed, which is inspired from tactile sensing in humans for building artificial somatosensory maps in robots. Experiments in simulation are used to validate the approach.
The Ego and the Id

The Ego and the Id ranks high among the works of Freud's later years. The heart of his concern is the ego, which he sees battling with three forces: the id, the super-ego, and the outside world. Of the various English translations of Freud's major works to appear in his lifetime, only one was authorized by Freud himself: The Standard Edition of the Complete Psychological Works of Sigmund Freud under the general editorship of James Strachey. Freud approved the overall editorial plan, specific renderings of key words and phrases, and the addition of valuable notes, from bibliographical and explanatory. Many of the translations were done by Strachey himself; the rest were prepared under his supervision. The result was to place the Standard Edition in a position of unquestioned supremacy over all other existing versions.
Privacy Preserving Maximum Consensus

Maximum consensus is useful in many applications such as leader selection and time synchronization, and it is advantageous for its decentralization and finite time convergence. However, without preservation mechanisms for maximum consensus, nodes' initial states and especially the identity of the node with the maximum initial state will be disclosed, which is undesirable in some application scenarios. To preserve the privacy of maximum consensus while maintaining its advantages, we propose a Privacy Preserving Maximum Consensus (PPMC) algorithm, where all nodes independently generate and transmit random numbers before sending out their initial states. We prove that PPMC converges in finite time. Meanwhile, explicit formulas are given to characterize the probability that the maximum state owner's identity is inferred by its neighbors. Extensive simulations are conducted to demonstrate the effectiveness of the proposed algorithm.
Possibilities of Androids as poetry-reciting agent

In recent years, research has increased on very human-like androids, generally investigating the following: (1) how people treat such very human-like androids and (2) whether it is possible to replace such existing communication media as telephones or TV conference systems with androids as a communication medium. We found that androids have advantages over humans in specific contexts. For example, in a collaboration theatrical project between artists and androids, audiences were impressed by the androids that read poetry. We, therefore, experimentally compared androids and humans in a poetry-reciting context by conducting an experiment to illustrate the influence of an android who recited poetry. Participants listened to poetry that was read by three poetry-reciting agents: the android, the human model on which the android was based, and a box. The experiment results showed that the enjoyment of the poetry gained the highest score under the android condition, indicating that the android has an advantage for communicating the meaning of poetry.
Vitamin dificiencies and neural tube defects.

Serum folate, red cell folate, white blood cell vitamin C, riboflavin saturation index, and serum vitamin A were determined during the first trimester of pregnancy in over 900 cases. For each of these there was a social classes I + II showed the highest levels which differed significantly from other classes, except for serum folate. In 6 mothers who gave birth to infants with neural tube defects, first trimester serum folate, red cell folate, white blood cell vitamin C, and riboflavin values were lower than in controls. In spite of small numbers the differences were significant for red cell folate (P less than 0-001) and white blood cell vitamin C (P less than 0-05). These findings are compatible with the hypothesis that nutritional deficiencies are significant in the causation of congenital defects of the neural tube in man.
Supply and demand in smart grid: A closed-loop pricing strategy

How to design a dynamic pricing strategy in smart grid is an important but challenging problem due to the uncertainty of customers' demand and their reaction to the price. Most of the existing pricing strategies depend on the prediction of customers' demand and their reaction to the price, thus are not robust enough due to the prediction which may cause a high cost to the supplier. In this paper, we propose a closed-loop pricing algorithm (CPA), which can largely decrease the cost and result in both costing savings for customers and higher profit for the supplier, and thus achieves a win-win solution. We provide sufficient conditions to guarantee the win-win solution for customers and the supplier. We also prove that CPA can obtain a stable price. Extensive simulations confirm with our analysis and show that the combined cost saving and profit gain of both customers and the supplier can be 76% by the proposed algorithm compared with the prediction-based pricing algorithm.
Caffeine Boosts Bees' Memories

Caffeine in floral nectar enhances the memory of bees for the flowers' scent by altering response properties of neurons in the bee brain. [Also see Report by Wright et al.] Pollination systems are biological markets, where flower visitors choose between flower species on the basis of their quality, such as the sweetness and amount of nectar per flower. Plants in turn compete for pollinators and advertise their product through colorful visual displays and scents. A key challenge in floral advertising is that signals must be not only attractive but also memorable (1): The more distinct a flower signal, the more likely a pollinator is to remember it, increasing the probability that pollinators will visit more flowers of this species while ignoring competing flower species. On page 1202 of this issue, Wright et al. (2) report that some plant species appear to gain an unfair advantage in this competitive market by manipulating the memory of bees with psychoactive drugs.
Sustainable Intensification in Agriculture: Premises and Policies

Clearer understanding is needed of the premises underlying SI and how it relates to food-system priorities. Food security is high on the global policy agenda. Demand for food is increasing as populations grow and gain wealth to purchase more varied and resource-intensive diets. There is increased competition for land, water, energy, and other inputs into food production. Climate change poses challenges to agriculture, particularly in developing countries (1), and many current farming practices damage the environment and are a major source of greenhouse gases (GHG). In an increasingly globalized world, food insecurity in one region can have widespread political and economic ramifications (2).
The Complexities of Genomic Identifiability

Recent work reveals the need to re-examine the current paradigms for managing the potential identifiability of genomic and other "omic"-type data. [Also see News story and Report by Gymrek et al.] Sharing research data has long been fundamental to the advancement of science. In today's scientific culture, making research data available broadly and efficiently via the internet has become the standard for many data types, including genomic and some other "omic"-type data produced by high-throughput methods. The acceleration of research progress and the resulting public benefit achieved through such broad data-sharing have been transformative for the scientific enterprise (1–3). However, sharing data generated from human research participants must be done in a manner that appropriately protects participant interests.
3D Reconstruction of the Source and Scale of Buried Young Flood Channels on Mars

Seeing Below the Surface Marte Vallis represents the largest of the young outflow channels on Mars. Thought to be the result of an ancient megaflood that occurred during a period that is otherwise known to be cold and dry, this channel system extends more than approximately 1000 kilometers in length and 100 kilometers in width. The channels' depths are unknown, however, because they have been covered by lava flows. By using the SHARAD radar sounder on the Mars Reconnaissance Orbiter, Morgan et al. (p. 607, published online 7 March) produced a three-dimensional reconstruction of the subsurface channels. The channels are twice as deep as previously thought and the floodwaters came from the Cerberus Fossae extensional fracture system. Radar data taken from orbit reveal the complex morphology of buried flood channels in a young region of Mars. Outflow channels on Mars are interpreted as the product of gigantic floods due to the catastrophic eruption of groundwater that may also have initiated episodes of climate change. Marte Vallis, the largest of the young martian outflow channels (<500 million years old), is embayed by lava flows that hinder detailed studies and comparisons with older channel systems. Understanding Marte Vallis is essential to our assessment of recent Mars hydrologic activity during a period otherwise considered to be cold and dry. Using data from the Shallow Radar sounder on the Mars Reconnaissance Orbiter, we present a three-dimensional (3D) reconstruction of buried channels on Mars and provide estimates of paleohydrologic parameters. Our work shows that Cerberus Fossae provided the waters that carved Marte Vallis, and it extended an additional 180 kilometers to the east before the emplacement of the younger lava flows. We identified two stages of channel incision and determined that channel depths were more than twice those of previous estimates.
R-Loop Stabilization Represses Antisense Transcription at the Arabidopsis FLC Locus

Making Antisense of Flowering The recent discovery of biological roles for long noncoding RNAs raises important questions as to how they are themselves regulated. Sun et al. (p. 619) adopted a genetic approach to identify regulators of COOLAIR—a set of antisense transcripts from the locus encoding the major Arabidopsis floral repressor, FLC. Analysis of a mutant misregulating COOLAIR revealed a homeodomain protein that repressed COOLAIR expression via an R-loop covering the COOLAIR promoter. Thus, R-loop stabilization is an integral part of COOLAIR regulation, FLC expression, and flowering time. A homeodomain protein limits expression of antisense transcripts involved in flowering time control. Roles for long noncoding RNAs (lncRNAs) in gene expression are emerging, but regulation of the lncRNA itself is poorly understood. We have identified a homeodomain protein, AtNDX, that regulates COOLAIR, a set of antisense transcripts originating from the 3′ end of Arabidopsis FLOWERING LOCUS C (FLC). AtNDX associates with single-stranded DNA rather than double-stranded DNA non–sequence-specifically in vitro, and localizes to a heterochromatic region in the COOLAIR promoter in vivo. Single-stranded DNA was detected in vivo as part of an RNA-DNA hybrid, or R-loop, that covers the COOLAIR promoter. R-loop stabilization mediated by AtNDX inhibits COOLAIR transcription, which in turn modifies FLC expression. Differential stabilization of R-loops could be a general mechanism influencing gene expression in many organisms.
Parenting Manuals on Underage Drinking

Abstract Background: There is some debate over the efficacy of alcohol industry parenting manuals. Purpose: This study compares the content and focus of alcohol industry and non-industry “talk to your child about drinking” parenting manuals. Methods: Parenting manuals from Anheuser-Busch and Miller Brewing Company were compared to federal government and private health agency manuals (e.g., the National Council on Alcoholism and Drug Dependence and a joint project by the Department of Health and Human Services and the Ad Council). Independent reviewers read each page from the manuals and coded how frequently alcohol-related problems and potentially sensitive public health perspectives were mentioned. Tabulations were converted in rates of mentions per 1000 words. Results: Although the industry parenting manuals analyzed in this study advised parents to “get the facts,” they provided substantially fewer reasons why teens should not drink and showed significantly lower rates of mention for most problems compared to non-industry manuals. They also avoided potentially sensitive public health perspectives on underage drinking, whereas the non-industry manuals devoted considerable attention to these issues. Discussion: This preliminary study suggests that when alcohol companies control the alcohol education agenda, major omissions are made, only selected risks are communicated, and the public health dimensions of the problem are minimized. Translation to Health Education Practice: Health educators should be aware of the vast range of topic coverage and focus available in parenting manuals on underage drinking when considering use of such material.
Evaluation of the Vitek 2 Korean Antimicrobial Susceptibility Testing Cards AST N056 and AST N055

Background: The recently issued Korean version of antimicrobial susceptibility cards for Vitek 2 system uses an adjusted antimicrobial combination that reflects Korean clinical practice and CLSI guidelines. We evaluated the two Korean antimicrobial susceptibility testing cards for gram negative rods, AST N056 and AST N055. Methods: The results of susceptibility tests were compared between the original and Korean cards. A number of the same antimicrobials included in the both cards were 15 in AST N041-AST N056 and 17 in AST N022-AST N055. Susceptibilities to the newly added antimicrobials, aztreonam, tobramycin, and meropenem for AST N056; and cefotaxime, levofloxacin, and minocycline for AST N055 were compared with those obtained by disc diffusion test and, in case of discrepancy, by confirmative Etest or broth dilution method. Results: In comparison between AST N041 and AST N056 cards, the average discrepancy rate per strain was 0.34, minor error was 88.2%, and major error and very major error were both 5.9%. In comparison between AST N022 and AST055 cards, the average discrepancy rate per strain and very major error were 1.23 and 4.4%, respectively. The three antimicrobial agents added into AST N055 card showed highly discrepant results as a total of 49 items (44.1%) in 111 isolates were discrepant with very major error of 5.9% and major error of 2.0%. Conclusion: AST N056 showed acceptable results in most items including the newly added antimicrobial agents. However, in the case of AST N055 card that showed a relatively high discrepancy, other indicator antibiotics should be referred to for newly added three antimicrobials. For the antibiotics that showed a high discrepancy between the original and Korean cards, a comparison study should be performed using the standard method and clinical isolates collected in Korea. (Korean J Clin Microbiol 2008;11:2328)