julilili42/papers huggingface dataset:
Biomass–density relationships of plant communities deviate from the self‐thinning rule due to age structure and abiotic stress
2020-06-02

A pertinent debate in plant ecology centers around the generality of the self‐thinning rule. However, studies focused on highly simplified settings such as even‐aged monospecific populations or optimal conditions. This neglects the fact that most natural communities, to which the classical self‐thinning slope is often applied, are age‐structured, composed of multiple species and exposed to various types of abiotic stress. With the help of an individual‐based model, we relax these simplified assumptions and systematically test for changes in the biomass–density relationships of uneven‐aged, functionally diverse plant communities across a complete stress gradient, using excessive to insufficient soil water as a case study. We show that frequent recruitment, which resulted in an uneven‐aged community, and stress intensity caused predictable changes in the entire biomass–density trajectory. Increasing stress resulted in steeper (more negative) slopes and increased the intercept in the classical self‐thinning section irrespective of excessive or insufficient soil water as a stress type. Recruitment steepened the slope, too and enabled a novel section in the biomass–density trajectory. This novel section represented a quasi‐steady state of the density‐dependent dynamics of new generations which occurred locally within patches of recruitment. At the community level, the slope of the biomass–density relationship at quasi‐steady state had a significantly flatter slope of −1.1 under optimal soil water conditions. Functional diversity showed little impact on density‐dependent mortality. Namely, it resulted in an earlier onset of mortality but not in changes in the values of the slope and intercept. We conclude that the classical −3/2 slope is not useful to describe the biomass–density relationship in natural and semi‐natural plant communities. The magnitude and direction of variation in the slope are related to the age‐structure and abiotic stress intensity in the plant community.
The Perception Engineer’s Toolkit for Eye-Tracking data analysis
2020-06-02

Tools for eye-tracking data analysis are as of now either provided as proprietary software by the eye-tracker manufacturer or published by researchers under licenses that are problematic for some use-cases (e.g., GPL3). This lead to repeated re-implementation of the most basic building blocks, such as event filters, often resulting in incomplete, incomparable and even erroneous implementations.
A gibberellin methyltransferase modulates the timing of floral transition at the Arabidopsis shoot meristem
2020-06-02

The transition from vegetative to reproductive growth is a key event in the plant life cycle. Plants therefore use a variety of environmental and endogenous signals to determine the optimal time for flowering to ensure reproductive success. These signals are integrated at the shoot apical meristem (SAM), which subsequently undergoes a shift in identity and begins producing flowers rather than leaves, while still maintaining pluripotency and meristematic function. Gibberellic acid (GA), an important hormone associated with cell growth and differentiation, has been shown to promote flowering in many plant species including Arabidopsis thaliana , but the details of how spatial and temporal regulation of GAs in the SAM contribute to floral transition are poorly understood. In this study, we show that the gene GIBBERELLIC ACID METHYLTRANSFERASE 2 ( GAMT2 ), which encodes a GA‐inactivating enzyme, is significantly upregulated at the SAM during floral transition and contributes to the regulation of flowering time. Loss of GAMT2 function leads to early flowering, whereas transgenic misexpression of GAMT2 in specific regions around the SAM delays flowering. We also found that GAMT2 expression is independent of the key floral regulator LEAFY but is strongly increased by the application of exogenous GA. Our results indicate that GAMT2 is a repressor of flowering that may act as a buffer of GA levels at the SAM to help prevent premature flowering.
Exploiting the GBVS for Saliency aware Gaze Heatmaps
2020-06-02

Analyzing visual perception in scene images is dominated by two different approaches: 1.) Eye Tracking, which allows us to measure the visual focus directly by mapping a detected fixation to a scene image, and 2.) Saliency maps, which predict the perceivability of a scene region by assessing the emitted visual stimulus with respect to the retinal feature extraction. One of the best-known algorithms for calculating saliency maps is GBVS. In this work, we propose a novel visualization method by generating a joint fixation-saliency heatmap. By incorporating a tracked gaze signal into the GBVS, the proposed method equilibrates the fixation frequency and duration to the scene stimulus, and thus visualizes the rate of the extracted visual stimulus by the spectator.
Dapsone is not a Pharmacodynamic Lead Compound for its Aryl Derivatives
2020-06-02

Background: The relatedness between the linear equations of thermodynamics and QSAR was studied thanks to the recently elucidated crystal structure complexes between sulfonamide pterin conjugates and dihydropteroate synthase (DHPS) together with a published set of thirty- six synthetic dapsone derivatives with their reported entropy-driven activity data. Only a few congeners were slightly better than dapsone. Objective : Our study aimed at demonstrating the applicability of thermodynamic QSAR and to shed light on the mechanistic aspects of sulfone binding to DHPS. Methods: To this end ligand docking to DHPS, quantum mechanical properties, 2D- and 3D-QSAR as well as Principle Component Analysis (PCA) were carried out. Results: The short aryl substituents of the docked pterin-sulfa conjugates were outward oriented into the solvent space without interacting with target residues which explains why binding enthalpy (ΔH) did not correlate with potency. PCA revealed how chemically informative descriptors are evenly loaded on the first three PCs (interpreted as ΔG, ΔH and ΔS), while chemically cryptic ones reflected higher dimensional (complex) loadings. Conclusions: It is safe to utter that synthesis efforts to introduce short side chains for aryl derivatization of the dapsone scaffold have failed in the past. On theoretical grounds we provide computed evidence why dapsone is not a pharmacodynamic lead for drug profiling because enthalpic terms do not change significantly at the moment of ligand binding to target.
The Vesicle Builder - A Membrane Packing Algorithm for the CELLmicrocosmos MembraneEditor
2020-06-02

For a long time, the major focus of membrane simulations was laid on rectangular membrane patches based on the fluid mosaic model. Because of the computational performance of today's computer hardware, it is now possible to generate and simulate larger structures, such as vesicles or micelles. Yet, there are no approaches available to generate these partly complex structures in a convenient and interactive way using WYSIWYG methods and exporting it to PDB format. The CELLmicrocosmos 2.2 MembraneEditor was originally developed for the interactive computation of heterogeneous rectangular membrane patches, solving 2.5D packing problems. Now, its packing capabilities were extended into the third dimension by introducing the Vesicle Builder which is optimized for the computation of vesicular mono- or bilayer membranes. The shape computation is based on an ellipsoid formula enabling the generation of vesicles featuring different lipid compositions, shapes and sizes. More complex shapes can be generated by combining different shapes. Moreover, extended shape customization is possible by modifying and extending the algorithm. Three application cases are discussed: 1) Different potential vesicular configurations including wavy, ellipsoid, enclosing and modular structures are modelled and shortly discussed; 2) To evaluate the compatibility of the Vesicle Builder with simulation tools, a three-component vesicle was modelled and successfully simulated. 3) To show the capability to generate large structures, a vesicle with a radius of 370 Å was generated, consisting of approx. 50,000 lipids and 2 million atoms, respectively. The MembraneEditor as well as the Vesicle Builder plugin can be downloaded from https://Cm2.CELLmicrocosmos.org
Large-scale color biases in the retinotopic functional architecture are region specific and shared across human brains
2020-06-02

Abstract Despite the functional specialization in visual cortex, there is growing evidence that the processing of chromatic and spatial visual features is intertwined. While past studies focused on visual field biases in retina and behaviour, large-scale dependencies between coding of color and retinotopic space are largely unexplored in the cortex. Here we asked whether spatial color biases are shared across different human observers, and whether they are idiosyncratic for distinct areas. We tested this by predicting the color a person was seeing using a linear classifier that has never been trained on chromatic responses from that same brain, solely by taking into account: (1) the chromatic responses in other individuals’ brains and (2) commonalities between the spatial coding in brains used for training and the test brain. We were able to predict the color (and luminance) of stimuli seen by an observer based on other subjects’ activity patterns in areas V1-V3, hV4 and LO1. In addition, we found that different colors elicited systematic, large-scale retinotopic biases that were idiosyncratic for distinct areas and common across brains. The area-specific spatial color codes and their conservation across individuals suggest functional or evolutionary organization pressures that remain to be elucidated. Significance statement Does a color elicit comparable neural activity in two different observers? We addressed these questions, which involved the central test to predict what color someone is seeing based on their brain activity if it is only known how other brains respond to color. We estimated the commonalities across brains in the way they respond to achromatic, spatial stimulation, which allowed us to retinotopically align different brain responses to each other in a common response space. In this space derived without any color responses we could decode across brains what color an observer was seeing and found that spatial color biases differed between areas. Our results demonstrate systematic dependencies between chromatic and visual field representations that are area-specific and preserved across observers.
Six Propositions against Ageism in the COVID-19 Pandemic
2020-06-03

The risk of developing severe illness from COVID-19 and of dying from it increases with age. This statistical association has led to numerous highly problematic policy suggestions and comments revealing underlying ageist attitudes and promoting age discrimination. Such attitudes are based on negative stereotypes on the health and functioning of older adults. As a result, the lives of older people are disvalued, including in possible triage situations and in the potential limitation of some measures against the spread of the pandemic to older adults. These outcomes are unjustified and unethical. We develop six propositions against the ageism underlying these suggestions to spur a more adequate response to the current pandemic in which the needs and dignity of older people are respected.
Relation of X-ray activity and rotation in M dwarfs and predicted time-evolution of the X-ray luminosity
2020-06-03

The relation of activity to rotation in M dwarfs is of high astrophysical interest because it provides observational evidence of the stellar dynamo, which is poorly understood for low-mass stars, especially in the fully convective regime. Previous studies have shown that the relation of X-ray activity to rotation consists of two different regimes: the saturated regime for fast-rotating stars and the unsaturated regime for slowly rotating stars. The transition between the two regimes lies at a rotation period of ∼10 d. We present here a sample of 14 M dwarf stars observed with XMM-Newton and Chandra, for which we also computed rotational periods from Kepler Two-Wheel (K2) Mission light curves. We compiled X-ray and rotation data from the literature and homogenized all data sets to provide the largest uniform sample of M dwarfs (302 stars) for X-ray activity and rotation studies to date. We then fit the relation between Lx − Prot using three different mass bins to separate partially and fully convective stars. We found a steeper slope in the unsaturated regime for fully convective stars and a nonconstant Lx level in the saturated regime for all masses. In the Lx/Lbol − RO space we discovered a remarkable double gap that might be related to a discontinuous period evolution. Then we combined the evolution of Prot predicted by angular momentum evolution models with our new results on the empirical Lx − Prot relation to provide an estimate for the age decay of X-ray luminosity. We compare predictions of this relationship with the actual X-ray luminosities of M stars with known ages from 100 Myr to a few billion years. We find remarkably good agreement between the predicted Lx and the observed values for partially convective stars. However, for fully convective stars at ages of a few billion years, the constructed Lx-age relation overpredicts the X-ray luminosity because the angular momentum evolution model underpredicts the rotation period of these stars. Finally, we examine the effect of different parameterizations for the Rossby number (RO) on the shape of the activity-rotation relation in Lx/Lbol − RO space, and we find that the slope in the unsaturated regime and the location of the break point of the dual power-law depend sensitively on the choice of RO.
Individual differences in visual attention: A short, reliable, open-source, and multilingual test of multiple object tracking in PsychoPy
2020-06-03

Individual differences in attentional abilities provide an interesting approach in studying visual attention as well as the relation of attention to other psychometric measures. However, recent research has demonstrated that many tasks from experimental research are not suitable for individual differences research, as they fail to capture these differences reliably. Here, we provide a test for individual differences in visual attention which relies on the multiple object tracking task (MOT). This test captures individual differences reliably in 6 to 15 min. Within the task, the participants have to maintain a set of targets (among identical distractors) across an interval of object motion. It captures the efficiency of attentional deployment. Importantly, this test was explicitly designed and tested for reliability under conditions that match those of most laboratory research (restricted sample of students, approximately n = 50). The test is free to use and runs fully under open-source software. In order to facilitate the application of the test, we have translated it into 16 common languages (Chinese, Danish, Dutch, English, Finnish, French, German, Italian, Japanese, Norwegian, Polish, Portuguese, Russian, Spanish, Swedish, and Turkish). The test can be downloaded at https://osf.io/qy6nb/ . We hope that this MOT test supports researchers whose field of study requires capturing individual differences in visual attention reliably.
Return-To-Play Decision Making in Team Sports Athletes. A Quasi-Naturalistic Scenario Study
2020-06-03

Competitive athletes act within cultures of risk in sports and often decide to return to sport despite having acute health problems. The outcomes of such risky return-to-play decisions can not only negatively affect their future health, but may also limit their sports performance or even upset their career paths. Following risk-management-decision theory with its focus on active risk defusing, we developed a model for understanding the process of return-to-play decision making from an athlete's perspective. Based on the method of active information search, a quasi-naturalistic return-to-play decision scenario was created in order to assess amateur team sport athletes' decision-making strategies. The main goals were to identify different information acquisition patterns and to analyze the influence of varying sporting consequences on decision making. A total of 72 competitive team sport athletes (36 females, 36 males, <i>m</i> = 25.7 years of age, 3rd to 6th league level) from three disciplines (volleyball, basketball, and handball) participated in the experimental study. Facing the same medical scenario (a partial tear of the supraspinatus tendon), athletes show different approaches to return-to-play decision making. The main focus is on the potential sporting consequences of withdrawal from competition due to injury, with only a few players favoring well-informed decisions based on thorough risk analysis. The athletes who chose the medically risky alternative to play hurt mostly employed strategies of active risk defusing, which got activated when severe sporting consequences were perceived. Those who chose to withdraw from competition primarily referred to maximin heuristic, particularly when social pressure to play was reduced. The findings can be used to improve rehabilitation-related communication and shared return-to-play decision making in sports.
Epilepsy-causing STX1B mutations translate altered protein functions into distinct phenotypes in mouse neurons
2020-06-03

Abstract Syntaxin 1B (STX1B) is a core component of the N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex that is critical for the exocytosis of synaptic vesicles in the presynapse. SNARE-mediated vesicle fusion is assisted by Munc18-1, which recruits STX1B in the auto-inhibited conformation, while Munc13 catalyses the fast and efficient pairing of helices during SNARE complex formation. Mutations within the STX1B gene are associated with epilepsy. Here we analysed three STX1B mutations by biochemical and electrophysiological means. These three paradigmatic mutations cause epilepsy syndromes of different severity, from benign fever-associated seizures in childhood to severe epileptic encephalopathies. An insertion/deletion (K45/RMCIE, L46M) mutation (STX1BInDel), causing mild epilepsy and located in the early helical Habc domain, leads to an unfolded protein unable to sustain neurotransmission. STX1BG226R, causing epileptic encephalopathies, strongly compromises the interaction with Munc18-1 and reduces expression of both proteins, the size of the readily releasable pool of vesicles, and Ca2+-triggered neurotransmitter release when expressed in STX1-null neurons. The mutation STX1BV216E, also causing epileptic encephalopathies, only slightly diminishes Munc18-1 and Munc13 interactions, but leads to enhanced fusogenicity and increased vesicular release probability, also in STX1-null neurons. Even though the synaptic output remained unchanged in excitatory hippocampal STX1B+/− neurons exogenously expressing STX1B mutants, the manifestation of clear and distinct molecular disease mechanisms by these mutants suggest that certain forms of epilepsies can be conceptualized by assigning mutations to structurally sensitive regions of the STX1B−Munc18-1 interface, translating into distinct neurophysiological phenotypes.
Transcranial Sonography Findings in Alzheimer’s Disease: A New Imaging Biomarker
2020-06-03

Abstract Objective To validate transcranial sonography (TCS) as a novel imaging tool for the assessment of medial temporal lobe (MTL) atrophy (MTA). Materials and Methods Participants with Alzheimer’s disease (AD, n = 30) and age-sex-matched controls (n = 30) underwent TCS and MRI. On TCS, MTL structures (choroidal fissure (CF) and temporal horn (TH)) were measured and combined to create an MTA score in sonography (MTA-S). Furthermore, both THs and the third ventricle were combined to form the ventricle enlargement score in sonography (VES-S). On MRI, the MTL was evaluated by linear measurements, MTA scale and hippocampal volumetry. Validation was performed by comparing imaging methods and the patient group. Results Intraclass correlations for CF and TH showed substantial intra/inter-rater reliability (&gt; 0.80). TCS and MRI showed strong to moderate correlation regarding TH (right = 0.88, left = 0.89) and CF (right = 0.70, left = 0.47). MTA-S correlated significantly with the hippocampal volume (right = –0.51, left = –0.47), predicted group membership in logistic regression (Exp(B) right = 3.0, left = 2.7), and could separate AD patients from controls (AUC = 0.93). An MTA-S of 6 mm and 10 mm discriminated MRI MTA scores 0–1 (from 2–4) and MTA score 4 (from 0–3) with 100 % specificity, respectively. VES-S also showed a moderate correlation with the hippocampal volume (r = –0.66) and could differentiate AD patients from controls (AUC = 0.93). Conclusion Our results suggest that TCS may be an alternative imaging tool for the assessment of MTL atrophy and ventricular enlargement for patients in whom MRI scanning is not possible. Additionally, TCS offers a practical, patient-friendly and inexpensive option for the screening and follow-up of individuals with AD.
Proteins and Molecular Pathways Relevant for the Malignant Properties of Tumor-Initiating Pancreatic Cancer Cells
2020-06-03

Cancer stem cells (CSCs), a small subset of the tumor bulk with highly malignant properties, are deemed responsible for tumor initiation, growth, metastasis, and relapse. In order to reveal molecular markers and determinants of their tumor-initiating properties, we enriched rare stem-like pancreatic tumor-initiating cells (TICs) by harnessing their clonogenic growth capacity in three-dimensional multicellular spheroid cultures. We compared pancreatic TICs isolated from three-dimensional tumor spheroid cultures with nontumor-initiating cells (non-TICs) enriched in planar cultures. Employing differential proteomics (PTX), we identified more than 400 proteins with significantly different expression in pancreatic TICs and the non-TIC population. By combining the unbiased PTX with mRNA expression analysis and literature-based predictions of pro-malignant functions, we nominated the two calcium-binding proteins S100A8 (MRP8) and S100A9 (MRP14) as well as galactin-3-binding protein LGALS3BP (MAC-2-BP) as putative determinants of pancreatic TICs. In silico pathway analysis followed by candidate-based RNA interference mediated loss-of-function analysis revealed a critical role of S100A8, S100A9, and LGALS3BP as molecular determinants of TIC proliferation, migration, and in vivo tumor growth. Our study highlights the power of combining unbiased proteomics with focused gene expression and functional analyses for the identification of novel key regulators of TICs, an approach that warrants further application to identify proteins and pathways amenable to drug targeting.