julilili42/papers huggingface dataset:
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core
2018-04-26

Abstract Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Release 2 of Version 1 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML, their encoding in XML (the eXtensible Markup Language), validation rules that determine the validity of an SBML document, and examples of models in SBML form. No design changes have been made to the description of models between Release 1 and Release 2; changes are restricted to the format of annotations, the correction of errata and the addition of clarifications. Other materials and software are available from the SBML project website at http://sbml.org/ .
Information asymmetries between parents and educators in German childcare institutions
2018-04-26

Economic theory predicts market failure in the market for early childhood education and care (ECEC) due to information asymmetries. We empirically investigate information asymmetries between parents and ECEC professionals in Germany, making use of a unique extension of the Socio-Economic Panel Study (SOEP). We compare quality perceptions by parents and by professionals across 734 institutions. We detect considerable information asymmetries that differ across quality measures but less so by parental socio-economic background or center characteristics. Both similarly contribute to explaining variations in the information gap. We conclude that information is not readily available to parents; an issue that should be addressed by policy-makers.
Twenty years of stereotype threat research: A review of psychological mediators.
2018-04-26

This systematic literature review appraises critically the mediating variables of stereotypethreat. A bibliographic search was conducted across electronic databases between 1995and 2015. The search identified 45 experiments from 38 articles and 17 unique proposedmediators that were categorized into affective/subjective (n = 6), cognitive (n = 7) and motivationalmechanisms (n = 4). Empirical support was accrued for mediators such as anxiety,negative thinking, and mind-wandering, which are suggested to co-opt working memoryresources under stereotype threat. Other research points to the assertion that stereotypethreatened individuals may be motivated to disconfirm negative stereotypes, which canhave a paradoxical effect of hampering performance. However, stereotype threat appearsto affect diverse social groups in different ways, with no one mediator providing unequivocalempirical support. Underpinned by the multi-threat framework, the discussion postulatesthat different forms of stereotype threat may be mediated by distinct mechanisms.
LiGe(SiMe3)3: A New Substituent for the Synthesis of Metalloid Tin Clusters from Metastable Sn(I) Halide Solutions
2018-04-26

The most fruitful synthetic route to metalloid tin clusters applies the disproportionation reaction of metastable Sn(I) halide solutions, whereby Si(SiMe3)3 is mostly used as the stabilizing substituent. Here, we describe the synthesis and application of the slightly modified substituent Ge(SiMe3)3, which can be used for the synthesis of metalloid tin clusters to give the neutral cluster Sn10[Ge(SiMe3)3]6 as well as the charged clusters {Sn10[Ge(SiMe3)3]5}− and {Sn10[Ge(SiMe3)3]4}2−. The obtained metalloid clusters are structurally similar to their Si(SiMe3)3 derivatives. However, differences with respect to the stability in solution are observed. Additionally, a different electronic situation for the tin atoms is realized as shown by 119mSn Mössbauer spectroscopy, giving further insight into the different kinds of tin atoms within the metalloid cluster {Sn10[Ge(SiMe3)3]4}2−. The synthesis of diverse derivatives gives the opportunity to check the influence of the substituent for further investigations of metalloid tin cluster compounds.
A Specific Glycogen Mobilization Strategy Enables Rapid Awakening of Dormant Cyanobacteria from Chlorosis
2018-04-27

Many organisms survive stressful conditions via entry into a dormant state that can be rapidly exited when the stressor disappears; this ability provides a strong selective advantage. In the cyanobacterium <i>Synechocystis</i> sp. PCC 6803, the exit from nitrogen chlorosis takes less than 48 h and is enabled by the impressive metabolic flexibility of these cyanobacteria, which pass through heterotrophic and mixotrophic phases before reentering photoautotrophic growth. Switching between these states requires delicate coordination of carbohydrate oxidation, CO<sub>2</sub> fixation, and photosynthesis. Here, we investigated the contribution of the different carbon catabolic routes by assessing mutants of these pathways during nitrogen chlorosis and resuscitation. The addition of nitrate to nitrogen-starved cells rapidly starts the awakening program. Metabolism switches from maintenance metabolism, characterized by residual photosynthesis and low cellular ATP levels, to an initial heterotrophic phase, characterized by respiration and an immediate increase in ATP levels. This respiration relies on glycogen breakdown catalyzed by the glycogen phosphorylase GlgP2. In the following transient mixotrophic phase, photosynthesis and CO<sub>2</sub> fixation restart and glycogen is consumed. During the mixotrophic phase, parallel operation of the oxidative pentose phosphate cycle and the Entner-Doudoroff pathway is required for resuscitation to proceed; the glycolytic route via the Embden-Meyerhof-Parnas pathway has minor importance. Our data suggest that, during resuscitation, only the Entner-Doudoroff and oxidative pentose phosphate pathways supply the metabolic intermediates necessary for the anabolic reactions required to reconstitute a vegetative cell. Intriguingly, the key enzymes for glycogen catabolism are already expressed during the preceding chlorotic phase, in apparent preparation for rapid resuscitation.
Change in the gender division of domestic work after mothers or fathers took leave: exploring alternative explanations
2018-04-27

This study investigates how the durations of childcare leaves taken by mothers and fathers in Germany relate to the gender division of housework and childcare after labour market return. It examines to what extent changes in economic resources because of leave take-up may account for adaptations in the division of domestic work of dual-earner couples. Using data from the German Socio-Economic Panel (1992–2012) on about 800 couples with a first or second birth, we applied OLS regression models with lagged dependent variables. The results suggested that dual-earner couples where mothers took longer leaves experienced a greater shift towards a gender-traditional division of domestic labour after childbirth. Fathers' leave take-up was associated with a more equal division of family work. Lower relative earnings, e.g. as a result of changes in job-related skills after the leave, did not account for the shift in the gender division of family work.
Determining the Best Immunization Strategy for Protecting African Children Against Invasive Salmonella Disease
2018-04-27

Abstract Background The World Health Organization recently prequalified a typhoid conjugate vaccine (TCV), recommending its use in persons ≥6 months to 45 years residing in typhoid fever (TF)–endemic areas. We now need to consider how TCVs can have the greatest impact in the most vulnerable populations. Methods The Typhoid Fever Surveillance in Africa Program (TSAP) was a blood culture-based surveillance of febrile patients from defined populations presenting at healthcare facilities in 10 African countries. TF and invasive non-typhoidal Salmonella (iNTS) disease incidences were estimated for 0–10 year-olds in one-year age increments. Results Salmonella Typhi and iNTS were the most frequently isolated pathogens; 135 and 94 cases were identified, respectively. Analysis from three countries was excluded (incomplete person-years of observation (PYO) data). Thirty-seven of 123 TF cases (30.1%) and 71/90 iNTS disease cases (78.9%) occurred in children aged &amp;lt;5 years. No TF and 8/90 iNTS infections (8.9%) were observed in infants aged &amp;lt;9 months. The TF incidences (/100 000 PYO) for children aged &amp;lt;1 year and 1 to &amp;lt;2 years were 5 and 39, respectively; the highest incidence was 304 per 100 000 PYO in 4 to &amp;lt;5 year-olds. The iNTS disease incidence in the defined age groups ranged between 81 and 233 per 100 000 PYO, highest in 1 to &amp;lt;2 year-olds. TF and iNTS disease incidences were higher in West Africa. Conclusions High burden of TF detected in young children strengthens the need for TCV introduction. Given the concurrent iNTS disease burden, development of a trivalent vaccine against S. Typhi, S. Typhimurium, and S. Enteritidis may be timely in this region.
Primary Tactile Thalamus Spiking Reflects Cognitive Signals
2018-04-27

Little is known about whether information transfer at primary sensory thalamic nuclei is modified by behavioral context. Here we studied the influence of previous decisions/rewards on current choices and preceding spike responses of ventroposterior medial thalamus (VPm; the primary sensory thalamus in the rat whisker-related tactile system). We trained head-fixed rats to detect a ramp-like deflection of one whisker interspersed within ongoing white noise stimulation. Using generative modeling of behavior, we identify two task-related variables that are predictive of actual decisions. The first reflects task engagement on a local scale (“trial history”: defined as the decisions and outcomes of a small number of past trials), whereas the other captures behavioral dynamics on a global scale (“satiation”: slow dynamics of the response pattern along an entire session). Although satiation brought about a slow drift from Go to NoGo decisions during the session, trial history was related to local (trial-by-trial) patterning of Go and NoGo decisions. A second model that related the same predictors first to VPm spike responses, and from there to decisions, indicated that spiking, in contrast to behavior, is sensitive to trial history but relatively insensitive to satiation. Trial history influences VPm spike rates and regularity such that a history of Go decisions would predict fewer noise-driven spikes (but more regular ones), and more ramp-driven spikes. Neuronal activity in VPm, thus, is sensitive to local behavioral history, and may play an important role in higher-order cognitive signaling. SIGNIFICANCE STATEMENT It is an important question for perceptual and brain functions to find out whether cognitive signals modulate the sensory signal stream and if so, where in the brain this happens. This study provides evidence that decision and reward history can already be reflected in the ascending sensory pathway, on the level of first-order sensory thalamus. Cognitive signals are relayed very selectively such that only local trial history (spanning a few trials) but not global history (spanning an entire session) are reflected.
Frequency spectrum of an optical resonator in a curved spacetime
2018-04-27

The effect of gravity and proper acceleration on the frequency spectrum of an\\noptical resonator - both rigid or deformable - is considered in the framework\\nof general relativity. The optical resonator is modeled either as a rod of\\nmatter connecting two mirrors or as a dielectric rod whose ends function as\\nmirrors. Explicit expressions for the frequency spectrum are derived for the\\ncase that it is only perturbed slightly. For a deformable resonator, the\\nperturbation of the frequency spectrum depends on the speed of sound in the rod\\nsupporting the mirrors. A connection is found to a relativistic concept of\\nrigidity when the speed of sound approaches the speed of light. In contrast,\\nthe corresponding result for the assumption of Born rigidity is recovered when\\nthe speed of sound becomes infinite. The results presented in this article can\\nbe used as the basis for the description of optical and opto-mechanical systems\\nin a curved spacetime. We apply our results to the examples of a uniformly\\naccelerating resonator and an optical resonator in the gravitational field of a\\nsmall moving sphere. Our approach is not limited to weak gravitational fields,\\nwhich we exemplify by its application to the fictitious situation of an optical\\nresonator falling into a black hole.\\n
Hybrid cardiac imaging using PET/MRI: a joint position statement by the European Society of Cardiovascular Radiology (ESCR) and the European Association of Nuclear Medicine (EANM)
2018-04-27

Abstract Positron emission tomography (PET) and magnetic resonance imaging (MRI) have both been used for decades in cardiovascular imaging. Since 2010, hybrid PET/MRI using sequential and integrated scanner platforms has been available, with hybrid cardiac PET/MR imaging protocols increasingly incorporated into clinical workflows. Given the range of complementary information provided by each method, the use of hybrid PET/MRI may be justified and beneficial in particular clinical settings for the evaluation of different disease entities. In the present joint position statement, we critically review the role and value of integrated PET/MRI in cardiovascular imaging, provide a technical overview of cardiac PET/MRI and practical advice related to the cardiac PET/MRI workflow, identify cardiovascular applications that can potentially benefit from hybrid PET/MRI, and describe the needs for future development and research. In order to encourage its wide dissemination, this article is freely accessible on the European Radiology and European Journal of Hybrid Imaging web sites. • Studies and case-reports indicate that PET/MRI is a feasible and robust technology. • Promising fields of application include a variety of cardiac conditions. • Larger studies are required to demonstrate its incremental and cost-effective value. • The translation of novel radiopharmaceuticals and MR-sequences will provide exciting new opportunities.
A Vitamin E-Enriched Antioxidant Diet Interferes with the Acute Adaptation of the Liver to Physical Exercise in Mice
2018-04-28

Physical exercise is beneficial for general health and is an effective treatment for metabolic disorders. Vitamin E is widely used as dietary supplement and is considered to improve non-alcoholic fatty liver disease by reducing inflammation and dyslipidemia. However, increased vitamin E intake may interfere with adaptation to exercise training. Here, we explored how vitamin E alters the acute exercise response of the liver, an organ that plays an essential metabolic role during physical activity. Mice fed a control or an α-tocopherol-enriched diet were subjected to a non-exhaustive treadmill run. We assessed the acute transcriptional response of the liver as well as glucocorticoid signalling and plasma free fatty acids (FFA) and performed indirect calorimetry. Vitamin E interfered with the exercise-induced increase in FFA and upregulation of hepatic metabolic regulators, and it shifted the transcriptional profile of exercised mice towards lipid and cholesterol synthesis while reducing inflammation. Energy utilization, as well as corticosterone levels and signalling were similar, arguing against acute differences in substrate oxidation or glucocorticoid action. Our results show that high-dose vitamin E alters the metabolic and inflammatory response of the liver to physical exercise. The interference with these processes may suggest a cautious use of vitamin E as dietary supplement.
Multi-omics approach identifies novel pathogen-derived prognostic biomarkers in patients withPseudomonas aeruginosabloodstream infection
2018-04-28

Abstract Pseudomonas aeruginosa is a human pathogen that causes health-care associated blood stream infections (BSI). Although P. aeruginosa BSI are associated with high mortality rates, the clinical relevance of pathogen-derived prognostic biomarker to identify patients at risk for unfavorable outcome remains largely unexplored. We found novel pathogen-derived prognostic biomarker candidates by applying a multi-omics approach on a multicenter sepsis patient cohort. Multi-level Cox regression was used to investigate the relation between patient characteristics and pathogen features (2298 accessory genes, 1078 core protein levels, 107 parsimony-informative variations in reported virulence factors) with 30-day mortality. Our analysis revealed that presence of the helP gene encoding a putative DEAD-box helicase was independently associated with a fatal outcome (hazard ratio 2.01, p = 0.05). helP is located within a region related to the pathogenicity island PAPI-1 in close proximity to a pil gene cluster, which has been associated with horizontal gene transfer. Besides helP , elevated protein levels of the bacterial flagellum protein FliL (hazard ratio 3.44, p &lt; 0.001) and of a bacterioferritin-like protein (hazard ratio 1.74, p = 0.003) increased the risk of death, while high protein levels of a putative aminotransferase were associated with an improved outcome (hazard ratio 0.12, p &lt; 0.001). The prognostic potential of biomarker candidates and clinical factors was confirmed with different machine learning approaches using training and hold-out datasets. The helP genotype appeared the most attractive biomarker for clinical risk stratification due to its relevant predictive power and ease of detection.
Katharsis of the skin: peeling applications and agents of chemical peelings in Greek medical textbooks of Graeco‐Roman antiquity
2018-04-28

Abstract Background Recipes for peelings date back to medical texts of old Egypt. The oldest medical papyri contain recipes for ‘improving beauty of the skin’ and ‘removing wrinkles’ by use of agents such as salt and soda. The Egyptian Queen Cleopatra (69–30 BC ) is said to have taken bathes in donkey's milk to improve the beauty of her skin. However, little is known about other agents and peeling applications in later Greek medical textbooks. Objective We will discover new agents and describe ancient peeling applications. First, we will have to identify ancient Greek medical terms for the modern terms ‘peeling’ and ‘chemical peeling’. Second, on the basis of the identified terms, we will perform a systematic full‐text search for agents in original sources. Third, we will categorize the results into three peeling applications: (i) cleansing, (ii) aesthetical improvement of the skin and (iii) therapy of dermatological diseases. Methods We performed a full systematic keyword search with the identified Greek terms in databases of ancient Greek texts. Our keywords for peeling and chemical peeling are ‘smēxis’ and ‘trīpsis’. Our keywords for agents of peeling and chemical peeling are ‘smégmata’, ‘rhýmmata’, ‘kathartiká’ and ‘trímmata’. Results Diocles (4th century BC ) was the first one who mentioned ‘smēxis’ and ‘trīpsis’ as parts of daily cleansing routine. Criton (2nd century AD ) wrote about peeling applications, but any reference to the agents is lost. Antyllus (2nd century AD ) composed three lists of peeling applications including their agents. Conclusion Greek medical textbooks of Graeco‐Roman antiquity report several peeling applications such as cleansing, brightening, darkening, softening and aesthetical improvement of the skin by use of peeling and chemical peeling, as well as therapy of dermatological diseases. There are 27 ancient agents for what is contemporarily called peeling and chemical peeling. We discovered more specific agents than hitherto known to research.
Compressed sensing for high‐resolution nonlipid suppressed 1H FID MRSI of the human brain at 9.4T
2018-04-29

Purpose The aim of this study was to apply compressed sensing to accelerate the acquisition of high resolution metabolite maps of the human brain using a nonlipid suppressed ultra‐short TR and TE 1 H FID MRSI sequence at 9.4T. Methods X‐t sparse compressed sensing reconstruction was optimized for nonlipid suppressed 1 H FID MRSI data. Coil‐by‐coil x‐t sparse reconstruction was compared with SENSE x‐t sparse and low rank reconstruction. The effect of matrix size and spatial resolution on the achievable acceleration factor was studied. Finally, in vivo metabolite maps with different acceleration factors of 2, 4, 5, and 10 were acquired and compared. Results Coil‐by‐coil x‐t sparse compressed sensing reconstruction was not able to reliably recover the nonlipid suppressed data, rather a combination of parallel and sparse reconstruction was necessary (SENSE x‐t sparse). For acceleration factors of up to 5, both the low‐rank and the compressed sensing methods were able to reconstruct the data comparably well (root mean squared errors [RMSEs] ≤ 10.5% for Cre). However, the reconstruction time of the low rank algorithm was drastically longer than compressed sensing. Using the optimized compressed sensing reconstruction, acceleration factors of 4 or 5 could be reached for the MRSI data with a matrix size of 64 × 64. For lower spatial resolutions, an acceleration factor of up to R∼4 was successfully achieved. Conclusion By tailoring the reconstruction scheme to the nonlipid suppressed data through parameter optimization and performance evaluation, we present high resolution (97 μL voxel size) accelerated in vivo metabolite maps of the human brain acquired at 9.4T within scan times of 3 to 3.75 min.
The distribution of active iron‐cycling bacteria in marine and freshwater sediments is decoupled from geochemical gradients
2018-04-30

Summary Microaerophilic, phototrophic and nitrate‐reducing Fe(II)‐oxidizers co‐exist in coastal marine and littoral freshwater sediments. However, the in situ abundance, distribution and diversity of metabolically active Fe(II)‐oxidizers remained largely unexplored. Here, we characterized the microbial community composition at the oxic‐anoxic interface of littoral freshwater (Lake Constance, Germany) and coastal marine sediments (Kalø Vig and Norsminde Fjord, Denmark) using DNA‐/RNA‐based next‐generation 16S rRNA (gene) amplicon sequencing. All three physiological groups of neutrophilic Fe(II)‐oxidizing bacteria were found to be active in marine and freshwater sediments, revealing up to 0.2% anoxygenic photoferrotrophs (e.g., Rhodopseudomonas , Rhodobacter , Chlorobium ), 0.1% microaerophilic Fe(II)‐oxidizers (e.g., Mariprofundus , Hyphomona s, Gallionella ) and 0.3% nitrate‐reducing Fe(II)‐oxidizers (e.g., Thiobacillus , Pseudomonas , Denitromonas, Hoeflea ). Active Fe(III)‐reducing bacteria (e.g., Shewanella, Geobacter ) were most abundant (up to 2.8%) in marine sediments and co‐occurred with cable bacteria (up to 4.5%). Geochemical profiles of Fe(III), Fe(II), O 2 , light, nitrate and total organic carbon revealed a redox stratification of the sediments and explained 75%–85% of the vertical distribution of microbial taxa, while active Fe‐cycling bacteria were found to be decoupled from geochemical gradients. We suggest that metabolic flexibility, microniches in the sediments, or interrelationships with cable bacteria might explain the distribution patterns of active Fe‐cycling bacteria.