julilili42/papers huggingface dataset:
Substrate-dependent CO2 fixation in heterotrophic bacteria revealed by stable isotope labelling
2020-05-01

ABSTRACT Virtually all heterotrophs incorporate carbon dioxide by anaplerotic fixation. Little explored, however, is the interdependency of pathways and rates of CO2fixation on the concurrent usage of organic substrate(s). Potentially, this could reveal which substrates out of a pool of dissolved organic carbon are utilised by environmental microorganisms. To explore this possibility, Bacillus subtilis W23 was grown in a minimal medium with normalised amounts of either glucose, lactate or malate as only organic substrates, each together with 1 g/L NaH13CO3. Incorporation of H13CO3− was traced by elemental analysis-isotope ratio mass spectrometry of biomass and gas chromatography-mass spectrometry of protein-derived amino acids. Until the late logarithmic phase, 13C incorporation into the tricarboxylic acid cycle increased with time and occurred via [4–13C]oxaloacetate formed by carboxylation of pyruvate. The levels of 13C incorporation were highest for growth on glucose and lowest on malate. Incorporation of 13C into gluconeogenesis products was mainly detected in the lactate and malate experiment, whereas glucose down-regulated this path. A proof-of-principle study with a natural groundwater community confirmed the ability to determine incorporation from H13CO3− by natural communities leading to specific labelling patterns. This underlines the potential of the labelling approach to characterise carbon sources of heterotrophic microorganisms in their natural environments.
Birth of convective low-mass to high-mass second Larson cores
2020-05-01

Context. Stars form as an end product of the gravitational collapse of cold, dense gas in magnetized molecular clouds. This fundamentally multi-scale scenario occurs via the formation of two quasi-hydrostatic Larson cores and involves complex physical processes, which require a robust, self-consistent numerical treatment. Aims. The primary aim of this study is to understand the formation and evolution of the second hydrostatic Larson core and the dependence of its properties on the initial cloud core mass. Methods. We used the PLUTO code to perform high-resolution, one- and two-dimensional radiation hydrodynamic (RHD) core collapse simulations. We include self-gravity and use a grey flux-limited diffusion approximation for the radiative transfer. Additionally, we use for the gas equation of state density- and temperature-dependent thermodynamic quantities (heat capacity, mean molecular weight, etc.) to account for effects such as dissociation of molecular hydrogen, ionisation of atomic hydrogen and helium, and molecular vibrations and rotations. Properties of the second core are investigated using one-dimensional studies spanning a wide range of initial cloud core masses from 0.5 M ⊙ to 100 M ⊙ . Furthermore, we expand to two-dimensional (2D) collapse simulations for a selected few cases of 1 M ⊙ , 5 M ⊙ , 10 M ⊙ , and 20 M ⊙ . We follow the evolution of the second core for ≥100 years after its formation, for each of these non-rotating cases. Results. Our results indicate a dependence of several second core properties on the initial cloud core mass. Molecular cloud cores with a higher initial mass collapse faster to form bigger and more massive second cores. The high-mass second cores can accrete at a much faster rate of ≈10 −2 M ⊙ yr −1 compared to the low-mass second cores, which have accretion rates as low as 10 −5 M ⊙ yr −1 . For the first time, owing to a resolution that has not been achieved before, our 2D non-rotating collapse studies indicate that convection is generated in the outer layers of the second core, which is formed due to the gravitational collapse of a 1 M ⊙ cloud core. Additionally, we find large-scale oscillations of the second accretion shock front triggered by the standing accretion shock instability, which has not been seen before in early evolutionary stages of stars. We predict that the physics within the second core would not be significantly influenced by the effects of magnetic fields or an initial cloud rotation. Conclusions. In our 2D RHD simulations, we find convection being driven from the accretion shock towards the interior of the second Larson core. This supports an interesting possibility that dynamo-driven magnetic fields may be generated during the very early phases of low-mass star formation.
Spin Detection in Robotic Table Tennis
2020-05-01

In table tennis, the rotation (spin) of the ball plays a crucial role. A table tennis match will feature a variety of strokes. Each generates different amounts and types of spin. To develop a robot that can compete with a human player, the robot needs to detect spin, so it can plan an appropriate return stroke. In this paper we compare three methods to estimate spin. The first two approaches use a high-speed camera that captures the ball in flight at a frame rate of 380 Hz. This camera allows the movement of the circular brand logo printed on the ball to be seen. The first approach uses background difference to determine the position of the logo. In a second alternative, we train a CNN to predict the orientation of the logo. The third method evaluates the trajectory of the ball and derives the rotation from the effect of the Magnus force. This method gives the highest accuracy and is used for a demonstration. Our robot successfully copes with different spin types in a real table tennis rally against a human opponent.
Description of Citrobacter cronae sp. nov., isolated from human rectal swabs and stool samples
2020-05-01

Nine independent Gram-negative bacterial strains were isolated from rectal swabs or stool samples of immunocompromised patients from two different wards of a university hospital. All isolates were phylogenetically analysed based on their 16S rRNA gene sequence, housekeeping gene recN , multilocus sequence analysis of concatenated partial fusA , leuS , pyrG and rpoB sequences, and by whole genome sequencing data. The analysed strains of the new species cluster together and form a separate branch with Citrobacter werkmanii NBRC105721 T as the most closely related species. An average nucleotide identity value of 95.9–96% and computation of digital DNA–DNA hybridization values separate the new species from all other type strains of the genus Citrobacter . Biochemical characteristics further delimit the isolates from closely related Citrobacter type strains. As a result of the described data, a new Citrobacter species is introduced, for which the name Citrobacter cronae sp. nov. is proposed. The type strain is Tue2-1 T with a G+C DNA content of 52.2 mol%.
Derivation of input-output functions from distortion-product otoacoustic emission level maps
2020-05-01

Distortion-product otoacoustic emissions (DPOAEs) emerge from the cochlea when elicited with two tones of frequencies f1 and f2. DPOAEs mainly consist of two components, a nonlinear-distortion and a coherent-reflection component. Input-output (I/O) functions of DPOAE pressure at the cubic difference frequency, fDP=2f1−f2, enable the computation of estimated distortion-product thresholds (EDPTs), offering a noninvasive approach to estimate auditory thresholds. However, wave interference between the DPOAE components and suboptimal stimulus-level pairs reduces the accuracy of EDPTs. Here, the amplitude P of the nonlinear-distortion component is extracted from short-pulse DPOAE time signals. DPOAE level maps representing the growth behavior of P in L1,L2 space are recorded for 21 stimulus-level pairs and 14 frequencies with f2=1 to 14 kHz (f2/f1=1.2) from 20 ears. Reproducing DPOAE growth behavior using a least-squares fit approach enables the derivation of ridge-based I/O functions from model level maps. Objective evaluation criteria assess the fit results and provide EDPTs, which correlate significantly with auditory thresholds (p &amp;lt; 0.001). In conclusion, I/O functions derived from model level maps provide EDPTs with high precision but without the need of predefined optimal stimulus-level pairs.
Trust within sport NGB boards: association with board structure and board member characteristics
2020-05-01

Research question: Trust is a critical element within organisational and management literature. It reflects the decisions and behaviour of individual actors and the functioning of organisations and their management bodies. However, within the sport governance literature there is a notable absence of work focusing on trust. This study examines the association of trust and structural features within national governing bodies' (NGBs) boards.Research methods: 242 board members of 65 NGBs from Germany participated in an online survey which comprised questions on trust indicators and boards' structural features. Probit models were employed to analyse the association between trust indicators, individual board membership characteristics, and the boards' structural features.Results and findings: Results suggest that trust is a multifaceted phenomenon, affected by various (beneficial and detrimental) variables in the specific context of NGB boards. The study makes numerous interrelation and governance dynamics recognisable, with board size, board members' skill differentiation and temporal stability of boards appearing to be particularly relevant.Implications: The paper complements the professionalisation literature and the leadership discussion in the context of sport governance, particularly with regard to trust-enhancing working conditions within boards. The study also aligns to the good governance literature, revealing that in some respects the issue may be seen to be about trade-offs between trust-based effects and their resultant (positive or negative) outcomes for organisation, board or individual.
Probing the Magnetic Field in the GW170817 Outflow Using H.E.S.S. Observations
2020-05-01

Abstract The detection of the first electromagnetic counterpart to the binary neutron star (BNS) merger remnant GW170817 established the connection between short γ -ray bursts and BNS mergers. It also confirmed the forging of heavy elements in the ejecta (a so-called kilonova) via the r-process nucleosynthesis. The appearance of nonthermal radio and X-ray emission, as well as the brightening, which lasted more than 100 days, were somewhat unexpected. Current theoretical models attempt to explain this temporal behavior as either originating from a relativistic off-axis jet or a kilonova-like outflow. In either scenario, there is some ambiguity regarding how much energy is transported in the nonthermal electrons versus the magnetic field of the emission region. Combining the Very Large Array (radio) and Chandra (X-ray) measurements with observations in the GeV–TeV domain can help break this ambiguity, almost independently of the assumed origin of the emission. Here we report for the first time on deep H.E.S.S. observations of GW170817/GRB 170817A between 124 and 272 days after the BNS merger with the full H.E.S.S. array of telescopes, as well as on an updated analysis of the prompt (&lt;5 days) observations with the upgraded H.E.S.S. phase-I telescopes. We discuss implications of the H.E.S.S. measurement for the magnetic field in the context of different source scenarios.
Real-Time Graph-Based SLAM with Occupancy Normal Distributions Transforms
2020-05-01

Simultaneous Localization and Mapping (SLAM) is one of the basic problems in mobile robotics. While most approaches are based on occupancy grid maps, Normal Distributions Transforms (NDT) and mixtures like Occupancy Normal Distribution Transforms (ONDT) have been shown to represent sensor measurements more accurately. In this work, we slightly re-formulate the (O)NDT matching function such that it becomes a least squares problem that can be solved with various robust numerical and analytical non-linear optimizers. Further, we propose a novel global (O)NDT scan matcher for loop closure. In our evaluation, our NDT and ONDT methods are able to outperform the occupancy grid map based ones we adopted from Google's Cartographer implementation.
Wetland Distribution Trends in Central Asia
2020-05-01

Anthropogenic activities and climate change contribute to the deterioration of wetlands worldwide with Central Asia (CA) being among the regions which are most severely affected. This study examined how the distribution of wetlands in CA has changed in the last two decades. Emphasis was put on inland wetlands protected as International Bird and Biodiversity Areas. Time series of maps of wetlands (i.e. reed beds) were created for the years 2000, 2005, 2010, 2015 and 2018. A supervised classification approach was applied using NDVI of MODIS satellite images with 1000m resolution for the respective years. Ground control points were acquired through fieldtrips to the lower Chu River, upper Ili River and Ili River Delta in Kazakhstan and the Amu Darya River Delta and the Lower Amu Darya State Biosphere Reserve in Uzbekistan. The applied method is not applicable for the classification of wetlands in northern Kazakhstan. The vegetation there is too alike to the wetland vegetation in terms of values and seasonality of NDVI. For the remaining part of the study area, the applied method delivers satisfying results. However, it is difficult to determine a general trend for most wetland areas since there is a large variability between years. This study marks a first attempt at examining wetlands in CA at a regional scale. The results provide a baseline for further, more detailed research through either fieldtrips or by using higher resolution remote sensing data.
An irregular hourglass pattern describes the tempo of phenotypic development in placental mammal evolution
2020-05-01

Organismal development is defined by progressive transformations that ultimately give rise to distinct tissues and organs. Thus, temporal shifts in ontogeny often reflect key phenotypic differences in phylogeny. Classical theory predicts that interspecific morphological divergence originates towards the end of embryonic or fetal life stages, i.e. the early conservation model. By contrast, the hourglass model predicts interspecific variation early and late in prenatal ontogeny, though with a phylogenetically similar mid-developmental period. This phylotypic period, however, remains challenging to define within large clades such as mammals. Thus, molecular and morphological tests on a mammalian hourglass have not been entirely congruent. Here, we report an hourglass-like pattern for mammalian developmental evolution. By comparing published data on the timing of 74 homologous characters across 51 placental species, we demonstrated that variation in the timing of development decreased late in embryogenesis––when organ formation is highly active. Evolutionary rates of characters related to this timeframe were lowest, coinciding with a phylotypic period that persisted well beyond the pharyngula ‘stage’. The trajectory culminated with elevated variation in a handful of fetal and perinatal characters, yielding an irregular hourglass pattern. Our study invites further quantification of ontogeny across diverse amniotes and thus challenges current ideas on the universality of developmental patterns.
Barriers to Obtaining Informed Consent on Shortterm Surgical Missions
2020-05-01

Background: Short-term surgical missions (STSMs) enable visiting surgeons to help address inequalities in the provision of surgical care in resource-limited settings. One criticism of STSMs is a failure to obtain informed consent from patients before major surgical interventions. We aim to use collective evidence to establish the barriers to obtaining informed consent on STSMs and in resource-limited settings and suggest practical solutions to overcome them. Methods: A systematic review was performed using PubMed and Web of Science databases and following Preferred Reporting Items for Systematic Review and Meta-Analysis guidelines. In addition to the data synthesized from the systematic review, we also include pertinent data from a recent long-term follow-up study in Ethiopia. Results: Of the 72 records screened, 11 studies were included in our review. The most common barrier to obtaining informed consent was a paternalistic approach to medicine and patient education. Other common barriers were a lack of ethics education among surgeons in low-income and middle-income countries, cultural beliefs toward healthcare, and language barriers between the surgeons and patients. Our experience of a decade of reconstructive surgery missions in Ethiopia corroborates this. In a long-term follow-up study of our head-and-neck patients, informed consent was obtained for 85% (n = 68) of patients over a 14-year period. Conclusions: This study highlights the main barriers to obtaining informed consent on STSMs and in the resource-limited setting. We propose a checklist that incorporates practical solutions to the most common barriers surgeons will experience, aimed to improve the process of informed consent on STSMs.
Relativistic reflection spectra of super-spinning black holes
2020-05-01

Abstract We construct a relativistic reflection model in a non-Kerr spacetime in which, depending on the value of the deformation parameter of the metric, there are black hole solutions with spin parameter <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mrow><mml:mo>|</mml:mo></mml:mrow><mml:msub><mml:mi>a</mml:mi><mml:mrow><mml:mrow /><mml:mo>∗</mml:mo></mml:mrow></mml:msub><mml:mrow><mml:mo>|</mml:mo><mml:mo>&gt;</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:mrow></mml:math> . We apply our model to fit Suzaku data of four Seyfert galaxies (Ton S180, Ark 120, 1H0419–577, and Swift J0501.9–3239). These galaxies host at the center supermassive black holes that were previously interpreted as near-extremal Kerr black holes. For Ton S180 and 1H0419–577, our measurements are still consistent with the Kerr hypothesis. For Ark 120 and Swift J0501.9–3239, the Kerr solution is not recovered at 3- <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>σ</mml:mi></mml:math> . We discuss our results and possible systematic uncertainties in the model.
Targeting the Water Network in Cyclin G‐Associated Kinase (GAK) with 4‐Anilino‐quin(az)oline Inhibitors
2020-05-01

Abstract Water networks within kinase inhibitor design and more widely within drug discovery are generally poorly understood. The successful targeting of these networks prospectively has great promise for all facets of inhibitor design, including potency and selectivity for the target. Herein, we describe the design and testing of a targeted library of 4‐anilinoquin(az)olines for use as inhibitors of cyclin G‐associated kinase (GAK). GAK cellular target engagement assays, ATP binding‐site modelling and extensive water mapping provide a clear route to access potent inhibitors for GAK and beyond.
Phenomenal Causality and Sensory Realism
2020-05-01

One of the most important tasks for humans is the attribution of causes and effects in all wakes of life. The first systematical study of visual perception of causality—often referred to as phenomenal causality—was done by Albert Michotte using his now well-known launching events paradigm. Launching events are the seeming collision and seeming transfer of movement between two objects—abstract, featureless stimuli (“objects”) in Michotte’s original experiments. Here, we study the relation between causal ratings for launching events in Michotte’s setting and launching collisions in a photorealistically computer-rendered setting. We presented launching events with differing temporal gaps, the same launching processes with photorealistic billiard balls, as well as photorealistic billiard balls with realistic motion dynamics, that is, an initial rebound of the first ball after collision and a short sliding phase of the second ball due to momentum and friction. We found that providing the normal launching stimulus with realistic visuals led to lower causal ratings, but realistic visuals together with realistic motion dynamics evoked higher ratings. Two-dimensional versus three-dimensional presentation, on the other hand, did not affect phenomenal causality. We discuss our results in terms of intuitive physics as well as cue conflict.
CTAP for Italian: Integrating Components for the Analysis of Italian into a Multilingual Linguistic Complexity Analysis Tool
2020-05-01

Linguistic complexity research being a very actively developing field, an increasing number of text analysis tools are created that use natural language processing techniques for the automatic extraction of quantifiable measures of linguistic complexity. While most tools are designed to analyse only one language, the CTAP open source linguistic complexity measurement tool is capable of processing multiple languages, making cross-lingual comparisons possible. Although it was originally developed for English, the architecture has been extended to support multi-lingual analyses. Here we present the Italian component of CTAP, describe its implementation and compare it to the existing linguistic complexity tools for Italian. Offering general text length statistics and features for lexical, syntactic, and morpho-syntactic complexity (including measures of lexical frequency, lexical diversity, lexical and syntactical variation, part-of-speech density), CTAP is currently the most comprehensive linguistic complexity measurement tool for Italian and the only one allowing the comparison of Italian texts to multiple other languages within one tool.
Re-augmentation of the Axilla Using a Turn-Over Flap – a New Approach for the Surgical Treatment of Secondary Lymphedema After Breast Cancer
2020-05-01

Abstract Introduction Scarring and volume reduction of the axillary space resulting in persistent lymphedema is a side effect of axillary treatment in breast cancer patients. The aim of this paper is to describe the reduction of lymphedema achieved with a turnover flap. Materials and Methods Between October 2016 and May 2018, five patients with grade 2 lymphedema following breast cancer therapy underwent reconstructive surgery with a turnover flap. Complete excision of the symptomatic axillary scar tissue followed by re-augmentation using a turnover flap was performed. Subsequently, all patients underwent breast reconstruction using a distant flap reconnected to the thoracodorsal vessels. The circumference of both arms, quality of life and pain were measured before and after surgery. Results An average reduction in pain in the ipsilateral arm from 6 to 1 on the numerical scale as well as an improvement in quality of life (2.8 vs. 7.0) was observed. A decrease in lymphedema especially in the upper arm was identified. No complications such as secondary bleeding, infections or flap loss were observed. Conclusion Complete removal of the axillary scar tissue after breast cancer treatment and re-augmentation of the axilla with a turnover flap results in a reduction in ipsilateral lymphedema and an improvement in pain and quality of life. We interpret these findings as a result of the physiological re-alignment of the lymphatic vessels combined with a lymph node-containing local transposition flap. Therefore, re-augmentation with a turnover flap could be an effective non-microsurgical alternative to lymph node transplantation.