julilili42/papers huggingface dataset:
Slaying the Serpent : Comparative Mythological Perspectives on Susanoo’s Dragon Fight
2018-03-01

In the “Slaying of the Great Eight-Headed Serpent,” one of the most iconographic episodes in Japanese myth, the god Susanoo rescues a maiden from a dragon and marries her. Comparing the Japanese narrative with international dragon-slayer tales, this essay draws attention to the dragon’s close connection to water and iron. It argues that myths have to be adapted to new circumstances in order to remain relevant to the group that transmits them. In the myth of Susanoo’s dragon fight, as related in the ancient chronicles Kojiki and Nihon shoki, these repeated adaptations are still visible as various layers of meaning. The essay illuminates some of these layers and connects them to cultural techniques such as wet-rice cultivation or metallurgy. This approach makes it possible to trace the evolution of the myth, which found its culmination in the written versions of the early eighth century.
Early career researchers: an interview with Yossi Yovel
2018-03-01

Yossi Yovel is an Assistant Professor at Tel-Aviv University, Israel, where he studies bat echolocation. He received his joint honours Bachelor's degree in Biology and Physics before moving to complete his PhD with Hans-Ulrich Schnitzler at University of Tübingen, Germany, in 2008. He then completed postdocs at the Weizmann Institute, Israel, and University of Chicago, USA.
Local Observation of Phase Segregation in Mixed-Halide Perovskite
2018-03-02

Mixed-halide perovskites have emerged as promising materials for optoelectronics due to their tunable band gap in the entire visible region. A challenge remains, however, in the photoinduced phase segregation, narrowing the band gap of mixed-halide perovskites under illumination thus restricting applications. Here, we use a combination of spatially resolved and bulk measurements to give an in-depth insight into this important yet unclear phenomenon. We demonstrate that photoinduced phase segregation in mixed-halide perovskites selectively occurs at the grain boundaries rather than within the grain centers by using shear-force scanning probe microscopy in combination with confocal optical spectroscopy. Such difference is further evidenced by light-biased bulk Fourier-transform photocurrent spectroscopy, which shows the iodine-rich domain as a minority phase coexisting with the homogeneously mixed phase during illumination. By mapping the surface potential of mixed-halide perovskites, we evidence the higher concentration of positive space charge near the grain boundary possibly provides the initial driving force for phase segregation, while entropic mixing dominates the reverse process. Our work offers detailed insight into the microscopic processes occurring at the boundary of crystalline perovskite grains and will support the development of better passivation strategies, ultimately allowing the processing of more environmentally stable perovskite films.
Making Thymus Visible: Understanding T-Cell Development from a New Perspective
2018-03-02

T-cell development is coupled with a highly ordered migratory pattern. Lymphoid progenitors must follow a precise journey; starting from the hematopoietic tissue, they move toward the thymus and then migrate into and out of distinct thymic microenvironments, where they receive signals and cues required for their differentiation into naïve T-cells. Knowing where, when, and how these cells make directional "decisions" is key to understanding T-cell development. Such insights can be gained by directly observing developing T-cells within their environment under various conditions and following specific experimental manipulations. In the last decade, several model systems have been developed to address temporal and spatial aspects of T-cell development using imaging approaches. In this perspective article, we discuss the advantages and limitations of these systems and highlight a particularly powerful <i>in vivo</i> model that has been recently established. This model system enables the migratory behavior of all thymocytes to be studied simultaneously in a noninvasive and quantitative manner, making it possible to perform systems-level studies that reveal fundamental principles governing T-cell dynamics during development and in disease.
Population-specific design of de-immunized protein biotherapeutics
2018-03-02

Immunogenicity is a major problem during the development of biotherapeutics since it can lead to rapid clearance of the drug and adverse reactions. The challenge for biotherapeutic design is therefore to identify mutants of the protein sequence that minimize immunogenicity in a target population whilst retaining pharmaceutical activity and protein function. Current approaches are moderately successful in designing sequences with reduced immunogenicity, but do not account for the varying frequencies of different human leucocyte antigen alleles in a specific population and in addition, since many designs are non-functional, require costly experimental post-screening. Here, we report a new method for de-immunization design using multi-objective combinatorial optimization. The method simultaneously optimizes the likelihood of a functional protein sequence at the same time as minimizing its immunogenicity tailored to a target population. We bypass the need for three-dimensional protein structure or molecular simulations to identify functional designs by automatically generating sequences using probabilistic models that have been used previously for mutation effect prediction and structure prediction. As proof-of-principle we designed sequences of the C2 domain of Factor VIII and tested them experimentally, resulting in a good correlation with the predicted immunogenicity of our model.
Rare compound heterozygous variants in PNKP identified by whole exome sequencing in a German patient with ataxia‐oculomotor apraxia 4 and pilocytic astrocytoma
2018-03-02

Ataxia-oculomotor apraxia type 4 (AOA4) is a rare autosomal recessive neurologic disorder. The phenotype is characterized by ataxia, oculomotor apraxia, peripheral neuropathy and dystonia. AOA4 is caused by biallelic pathogenic variants in the PNKP gene encoding a polynucleotide kinase 3'-phosphatase with an important function in DNA-damage repair. By whole exome sequencing, we identified 2 variants within the PNKP gene in a 27-year-old German woman with a clinical AOA phenotype combined with a cerebellar pilocytic astrocytoma diagnosed at 23 years of age. One variant, a duplication in exon 14 resulting in the frameshift c.1253_1269dup p.(Thr424fs*49), has previously been described as pathogenic, for example, in cases of AOA4. The second variant, representing a nonsense mutation in exon 17, c.1545C>G p.(Tyr515*), has not yet been described and is predicted to cause a loss of the 7 C-terminal amino acids. This is the first description of AOA4 in a patient with central European descent. Furthermore, the occurrence of a pilocytic astrocytoma has not been described before in an AOA4 patient. Our data demonstrate compound heterozygous PNKP germline variants in a German patient with AOA4 and provide evidence for a possible link with tumor predisposition. Localization of the 2 variants in human PNKP NP_009185.2. NM_007254.3:c.1253_1269dup p.(Thr424fs*49) is predicted to cause a frameshift within the kinase domain, NM_007254.3:c.1545C>G p.(Tyr515*) is predicted to cause loss of 2 C-terminal amino acids of the kinase domain and 5 additional C-terminal amino acids.
The draft provisions on antitrust fines in the Commission’s ECN+ Proposal
2018-03-02

Abstract On 22 March 2017, the Commission released its Proposal for a directive to empower the competition authorities of the Member States to be more effective enforcers (COM(2017) 142 final). With this effort to harmonise national public enforcement regimes, the Commission enters uncharted territory. Effectiveness is deemed to be fostered by the introduction of the economic entity doctrine as a unitary sanctioning concept throughout the Member States. As a complementing measure, the Proposal prescribes a more coherent standard for leniency in the European Competition Network. The present article ventures to evaluate these remedies. A preliminary hypothesis is that the Commission’s conviction of the economic entity doctrine to become the gold standard for antitrust enforcement is possibly based on tenuous ideas of effectiveness. Moreover, the introduction of a 10 % fine cap for any National Competition Authority irrespective of the size of the Member State can lead to highly disparate relative fining powers throughout the internal market. As to the leniency aspect, the present article will attempt to assess whether the Proposal taps the full potential for enhancement. As an alternative to the Commission’s suggestions the article elaborates on a one-stop-shop leniency principle. Such would go beyond the current Proposal in that it would render multiple leniency filings obsolete within the EU.
Dismantling a complex of anther smuts (Microbotryum) on carnivorous plants in the genusPinguicula
2018-03-04

The anther smuts of the genus Microbotryum are known from host plant species belonging to the Caryophyllaceae, Dipsacaceae, Lamiaceae, Lentibulariaceae, Montiaceae, and Primulaceae. Of these, the anther smuts on Caryophyllaceae, in particular on Silene spp., are best known because they include model organisms studied in many disciplines of fungal biology. For Microbotryum species parasitic on Caryophyllaceae, a high degree of host specificity was revealed and several cryptic species were described. In contrast, the host specificity within Microbotryum pinguiculae occurring in anthers of different Pinguicula species (Lentibulariaceae) has not been investigated in detail until now. The anther smuts on Pinguicula alpina, P. villosa, and P. vulgaris, on which M. pinguiculae was described, were analyzed using nuc rDNA ITS1-5.8S-ITS2 and nuc rDNA 28S D1-D2 sequences and morphology to determine if they belong to one polyphagous species or rather represent three host-specific species. The results of the morphological investigations revealed no decisive differences between the anther smuts on different Pinguicula species. However, genetic divergence and molecular phylogenetic analyses, which split the specimens according to host plant species, supported host specificity of the anther smuts on different Pinguicula species. Accordingly, in addition to Microbotryum pinguiculae s. str. on Pinguicula vulgaris, M. alpinum sp. nov. on P. alpina from Europe and M. liroi sp. nov. on P. villosa from Asia are described and illustrated.
Napping and morningness-eveningness
2018-03-04

Our main aim in this work was to investigate the difference in napping behavior in relation to morningness and eveningness. We assessed morningness, eveningness, habitual sleep-wake times and different measures of napping, namely, start time, end time and duration on both weekdays and weekend days. Napping start time did not differ between weekdays and weekends, but napping ended later on weekends. Morning affect positively and eveningness negatively were related to nap end on weekend, nap duration on weekdays/weekend, average nap duration, and midpoint of napping on free days (MNFc). Nap duration was related to morningness and eveningness, with evening-oriented people napping longer. Midpoint of sleep and midpoint of napping were also positively correlated. Further, longer naps do not seem to compensate for lack of sleep on weekdays. As a conclusion, we identified napping as a correlate of morningness, eveningness and midpoint of sleep.
The changing role of ornamental horticulture in alien plant invasions
2018-03-05

ABSTRACT The number of alien plants escaping from cultivation into native ecosystems is increasing steadily. We provide an overview of the historical, contemporary and potential future roles of ornamental horticulture in plant invasions. We show that currently at least 75% and 93% of the global naturalised alien flora is grown in domestic and botanical gardens, respectively. Species grown in gardens also have a larger naturalised range than those that are not. After the Middle Ages, particularly in the 18th and 19th centuries, a global trade network in plants emerged. Since then, cultivated alien species also started to appear in the wild more frequently than non‐cultivated aliens globally, particularly during the 19th century. Horticulture still plays a prominent role in current plant introduction, and the monetary value of live‐plant imports in different parts of the world is steadily increasing. Historically, botanical gardens – an important component of horticulture – played a major role in displaying, cultivating and distributing new plant discoveries. While the role of botanical gardens in the horticultural supply chain has declined, they are still a significant link, with one‐third of institutions involved in retail‐plant sales and horticultural research. However, botanical gardens have also become more dependent on commercial nurseries as plant sources, particularly in North America. Plants selected for ornamental purposes are not a random selection of the global flora, and some of the plant characteristics promoted through horticulture, such as fast growth, also promote invasion. Efforts to breed non‐invasive plant cultivars are still rare. Socio‐economical, technological, and environmental changes will lead to novel patterns of plant introductions and invasion opportunities for the species that are already cultivated. We describe the role that horticulture could play in mediating these changes. We identify current research challenges, and call for more research efforts on the past and current role of horticulture in plant invasions. This is required to develop science‐based regulatory frameworks to prevent further plant invasions.
Electroconductive Biohybrid Collagen/Pristine Graphene Composite Biomaterials with Enhanced Biological Activity
2018-03-05

Abstract Electroconductive substrates are emerging as promising functional materials for biomedical applications. Here, the development of biohybrids of collagen and pristine graphene that effectively harness both the biofunctionality of the protein component and the increased stiffness and enhanced electrical conductivity (matching native cardiac tissue) obtainable with pristine graphene is reported. As well as improving substrate physical properties, the addition of pristine graphene also enhances human cardiac fibroblast growth while simultaneously inhibiting bacterial attachment ( Staphylococcus aureus ). When embryonic‐stem‐cell‐derived cardiomyocytes (ESC‐CMs) are cultured on the substrates, biohybrids containing 32 wt% graphene significantly increase metabolic activity and cross‐striated sarcomeric structures, indicative of the improved substrate suitability. By then applying electrical stimulation to these conductive biohybrid substrates, an enhancement of the alignment and maturation of the ESC‐CMs is achieved. While this in vitro work has clearly shown the potential of these materials to be translated for cardiac applications, it is proposed that these graphene‐based biohybrid platforms have potential for a myriad of other applications—particularly in electrically sensitive tissues, such as neural and neural and musculoskeletal tissues.
How you behave in school predicts life success above and beyond family background, broad traits, and cognitive ability.
2018-03-05

In this study, we investigated the role of student characteristics and behaviors in a longitudinal study over a 50-year timespan (using a large U.S. representative sample of high school students). We addressed the question of whether behaviors in school have any long-lasting effects for one's later life. Specifically, we investigated the role of being a responsible student, interest in school, writing skills, and reading skills in predicting educational attainment, occupational prestige, and income 11 years (N = 81,912) and 50 years (N = 1,952) after high school. We controlled for parental socioeconomic status, IQ, and broad personality traits in all analyses. We found that student characteristics and behaviors in adolescence predicted later educational and occupational success above and beyond parental socioeconomic status, IQ, and broad personality traits. Having higher interest in school was related to higher educational attainment at years 11 and 50, higher occupational prestige at year 11, and higher income at year 50. Higher levels of being a responsible student were related to higher educational attainment and higher occupational prestige at years 11 and 50. This was the first longitudinal study to test the role of student characteristics and behaviors over and above broad personality traits. It highlights the potential importance of what students do in school and how they react to their experiences during that time. It also highlights the possibility that things that happen in specific periods of one's life may play out in ways far more significant than we expect. (PsycINFO Database Record
Redundancy in Anaerobic Digestion Microbiomes during Disturbances by the Antibiotic Monensin
2018-03-05

ABSTRACT The antibiotic monensin is fed to dairy cows to increase milk production efficiency. A fraction of this monensin is excreted into the cow manure. Previous studies have found that cow manure containing monensin can negatively impact the performance of anaerobic digesters, especially upon first introduction. Few studies have examined whether the anaerobic digester microbiome can adapt to monensin during the operating time. Here, we conducted a long-term time series study of four lab-scale anaerobic digesters fed with cow manure. We examined changes in both the microbiome composition and function of the anaerobic digesters when subjected to the dairy antibiotic monensin. In our digesters, monensin was not rapidly degraded under anaerobic conditions. The two anaerobic digesters that were subjected to manure from monensin feed-dosed cows exhibited relatively small changes in microbiome composition and function due to relatively low monensin concentrations. At higher concentrations of monensin, which we dosed directly to control manure (from dairy cows without monensin), we observed major changes in the microbiome composition and function of two anaerobic digesters. A rapid introduction of monensin to one of these anaerobic digesters led to the impairment of methane production. Conversely, more gradual additions of the same concentrations of monensin to the other anaerobic digester led to the adaptation of the anaerobic digester microbiomes to the relatively high monensin concentrations. A member of the candidate OP11 ( Microgenomates ) phylum arose in this anaerobic digester and appeared to be redundant with certain Bacteroidetes phylum members, which previously were dominating. IMPORTANCE Monensin is a common antibiotic given to dairy cows in the United States and is partly excreted with dairy manure. An improved understanding of how monensin affects the anaerobic digester microbiome composition and function is important to prevent process failure for farm-based anaerobic digesters. This time series study demonstrates how anaerobic digester microbiomes are inert to low monensin concentrations and can adapt to relatively high monensin concentrations by redundancy in an already existing population. Therefore, our work provides further insight into the importance of microbiome redundancy in maintaining the stability of anaerobic digesters.
Outcomes of left split graft transplantation in Europe: report from the European Liver Transplant Registry
2018-03-05

Split liver transplantation (SLT) has been widely adopted across Europe, resulting in remarkable reduction in the paediatric waiting-list mortality. Left split graft (LSG) is commonly used for paediatric recipients; however, deceased donor criteria selection are not universal. The aim of this study was to analyse the LSG outcome from the European Liver Transplant Registry and to identify risk factors for graft failure. Data from 1500 children transplanted in 2006-2014 with LSG from deceased donors were retrospectively analysed. Overall, graft losses were 343(22.9%) after 5 years from transplantation, 240(70.0%) occurred within the first 3 months. Estimated patient survival was 89.1% at 3 months and 82.9% at 5 years from SLT. Re-transplantation rate was 11.5%. At multivariable analysis, significant risk factors for graft failure at 3 months included the following: urgent SLT (HR = 1.73, P = 0.0012), recipient body weight ≤6 kg (HR = 1.91, P = 0.0029), donor age >50 years (HR = 1.87, P = 0.0039), and cold ischaemic time (CIT) [HR = 1.07 per hour, P = 0.0227]. LSG has good outcomes and SLT is excellent option for paediatric recipients in the current organ shortage era. We identified practical guidelines for LSG donor and recipient selection criteria: donor age may be safely extended up to 50 years in the absence of additional risk factors; thus, children <6 kg and urgent transplantation need CIT <6 h and appropriate graft/recipient size-matching to achieve good outcomes.
Imaging Organic–Mineral Aggregates Formed by Fe(II)-Oxidizing Bacteria Using Helium Ion Microscopy
2018-03-05

Helium ion microscopy (HIM) has been used to image the development of mineralized twisted stalks produced by a neutrophilic, microaerophilic Fe(II)-oxidizing bacteria of the class Zetaproteobacteria. HIM is a relatively new type of microscopy which has several advantages over conventional scanning electron microscopy (SEM) due to its higher spatial resolution and the fact that samples can be imaged without coating (e.g., with Pt/Au). Here, we use HIM to show the development of nanometer- and micrometer-sized twisted stalk features consisting of organic material and Fe(III) minerals which appear to be loosely bound to the bacterial cells. These appendages are thought to be essential for eliminating Fe(III) waste produced during Fe(II) oxidation by sorbing Fe(III) and transporting it away from the cell. The results show the initial formation of long, precipitate-free stalks. After just 2 days, these became encrusted with spiky lepidocrocite crystals, and by 1 month, the characteristic twisted shape was almost indiscernible. These results demonstrate the high quality of images which can be obtained with helium ion microscopy from organic and mineral structures produced by bacteria without the requirement to sputter coat samples with conductive metals and can thus be considered to be more representive of how these structures would exist in the environment.