julilili42/papers huggingface dataset:
Subduction Reversal in a Divergent Double Subduction Zone Drives the Exhumation of Southern Qiangtang Blueschist‐Bearing Mélange, Central Tibet
2020-03-18

Abstract (Ultra) high‐pressure (HP) rocks can be exhumed rapidly by subduction reversal or divergent plate motion. Recent studies show that subduction reversal can in particular occur in a divergent double subduction zone when the slab pull of one slab exceeds that of the other, shorter one, which then experiences a net upward pull. This recent hypothesis, first proposed for Triassic HP‐rocks exposed in the central Qiangtang mélange belt in central Tibet, can explain the exhumation of (ultra) HP rocks through upward slab movement. However, this model lacks the support of kinematic evidence. In this study, based on the recognition of multiple deformational phases, we analyze the kinematics of the HP‐bearing mélange in central Qiangtang. Based on new 40 Ar‐ 39 Ar geochronology data and those collected from the literature, we present a temporal framework for the new observations. We recognize a switch in sense of shear between the prograde (D1) and exhumation (D2‐3) paths. The change of shear sense reflects the reversal from downward to upward movement of the oceanic slab below. Early D2 represents the early exhumation stage that caused retrograde metamorphism from eclogite to blueschist facies. No magmatism occurred during this period. Continued exhumation from blueschist facies to greenschist facies resulted in D2‐D3 structures. Voluminous igneous activity occurred during this stage. We suggest that subduction reversal in a divergent double subduction zone can best explain the kinematic evolution and temporal framework above. This exhumation model may provide a new perspective on the exhumation mechanism for other HP rocks around the world.
Tropical Curves and Covers and Their Moduli Spaces
2020-03-18

Abstract Tropical geometry can be viewed as an efficient combinatorial tool to study degenerations in algebraic geometry. Abstract tropical curves are essentially metric graphs, and covers of tropical curves maps between metric graphs satisfying certain conditions. In this short survey, we offer an introduction to the combinatorial theory of abstract tropical curves and covers of curves, and their moduli spaces, and we showcase three results demonstrating how this theory can be applied in algebraic geometry.
Morphological thermodynamics for hard bodies from a controlled expansion
2020-03-18

The morphometric approach is a powerful ansatz for decomposing the chemical potential for a complex solute into purely geometrical terms. This method has proven accuracy in hard spheres, presenting an alternative to comparatively expensive (classical) density functional theory approaches. Despite this, fundamental questions remain over why it is accurate and how one might include higher-order terms to improve accuracy. We derive the morphometric approach as the exact resummation of terms in the virial series, providing further justification of the approach. The resulting theory is less accurate than previous morphometric theories, but provides fundamental insights into the inclusion of higher-order terms and to extensions to mixtures of convex bodies of arbitrary shape.
KRAS(G12C)–AMG 510 Interaction Dynamics Revealed by All-Atom Molecular Dynamics Simulations
2020-03-18

Supplementary material related to publication: KRAS(G12C)–AMG 510 Interaction Dynamics Revealed by All-Atom Molecular Dynamics Simulations. <em>Sci Rep</em> (2020) 10:11992 https://rdcu.be/b5Jf2 The <strong>.zip</strong> files contain full-length raw Desmond trajectories together with <strong>-out.cms</strong> topology files. The <strong>.mpg</strong> files are movies of each individual replica simulations. Simulation data in each file is the following: each 'Full' system replica (1–5) is a 10 μs MD simulation and each 'NAc' system replica (1–5) is a 5 μs MD simulation. The <strong>.pdb </strong>files contain the metastable state <strong><em>S</em><sub>1</sub></strong>–<strong><em>S</em><sub>4</sub> </strong>conformation coordinates (three conformations 01–03 for each state) and energy minimized PDB ID: 6oim structure (Protein Preparation Wizard, Schrödinger LLC). The pymol session file <strong>States.pse</strong> contains all the above .pdb structural coordinates in a single file.
Latitudinal effect of vegetation on erosion rates identified along western South America
2020-03-19

Erosion-vegetation interactions The impact of vegetation on erosion rates is hard to gauge. Although vegetation can hold soils in place mechanically, root systems can also loosen soils or even help to fracture rock. These processes can increase erosion, especially because areas of heavy vegetation tend to be in areas with high precipitation rates. Starke et al. tackled this issue using a large set of observations that span 3500 km of the Andes mountain range. They found a complex set of interactions where increasing vegetation decreases erosion in more arid regions but can accelerate erosion in vegetation dense regions. Science , this issue p. 1358
Dynamics of plasma biomarkers in Down syndrome: the relative levels of Aβ42 decrease with age, whereas NT1 tau and NfL increase
2020-03-19

Abstract Background Down syndrome (DS) is the most common genetic cause of Alzheimer’s disease (AD), but diagnosis of AD in DS is challenging due to the intellectual disability which accompanies DS. When disease-modifying agents for AD are approved, reliable biomarkers will be required to identify when and how long people with DS should undergo treatment. Three cardinal neuropathological features characterize AD, and AD in DS—Aβ amyloid plaques, tau neurofibrillary tangles, and neuronal loss. Here, we quantified plasma biomarkers of all 3 neuropathological features in a large cohort of people with DS aged from 3 months to 68 years. Our primary aims were (1) to assess changes in the selected plasma biomarkers in DS across age, and (2) to compare biomarkers measured in DS plasma versus age- and sex-matched controls. Methods Using ultra-sensitive single molecule array (Simoa) assays, we measured 3 analytes (Aβ42, NfL, and tau) in plasmas of 100 individuals with DS and 100 age- and sex-matched controls. Tau was measured using an assay (NT1) which detects forms of tau containing at least residues 6–198. The stability of the 3 analytes was established using plasma from ten healthy volunteers collected at 6 intervals over a 5-day period. Results High Aβ42 and NT1 tau and low NfL were observed in infants. Across all ages, Aβ42 levels were higher in DS than controls. Levels of Aβ42 decreased with age in both DS and controls, but this decrease was greater in DS than controls and became prominent in the third decade of life. NT1 tau fell in adolescents and young adults, but increased in older individuals with DS. NfL levels were low in infants, children, adolescents, and young adults, but thereafter increased in DS compared to controls. Conclusions High levels of Aβ42 and tau in both young controls and DS suggest these proteins are produced by normal physiological processes, whereas the changes seen in later life are consistent with emergence of pathological alterations. These plasma biomarker results are in good agreement with prior neuropathology studies and indicate that the third and fourth decades (i.e., 20 to 40 years of age) of life are pivotal periods during which AD processes manifest in DS. Application of the assays used here to longitudinal studies of individuals with DS aged 20 to 50 years of age should further validate the use of these biomarkers, and in time may allow identification and monitoring of people with DS best suited for treatment with AD therapies.
Drp1 modulates mitochondrial stress responses to mitotic arrest
2020-03-19

Abstract Antimitotic drugs are extensively used in the clinics to treat different types of cancer. They can retain cells in a prolonged mitotic arrest imposing two major fates, mitotic slippage, or mitotic cell death. While the former is molecularly well characterized, the mechanisms that control mitotic cell death remain poorly understood. Here, we performed quantitative proteomics of HeLa cells under mitotic arrest induced with paclitaxel, a microtubule-stabilizer drug, to identify regulators of such cell fate decision. We identified alterations in several apoptosis-related proteins, among which the mitochondrial fission protein Drp1 presented increased levels. We found that Drp1 depletion during prolonged mitotic arrest led to strong mitochondrial depolarization and faster mitotic cell death as well as enhanced mitophagy, a mechanism to remove damaged mitochondria. Our findings support a new role of Drp1 in orchestrating the cellular stress responses during mitosis, where mitochondrial function and distribution into the daughter cells need to be coordinated with cell fate. This novel function of Drp1 in the cell cycle becomes best visible under conditions of prolonged mitotic arrest.
Influence of Physical Activity Interventions on Body Representation: A Systematic Review
2020-03-19

Distorted representation of one's own body is a diagnostic criterion and corepsychopathology of disorders such as anorexia nervosa and body dysmorphic disorder. Previousliterature has raised the possibility of utilising physical activity intervention (PI) as atreatment option for individuals suffering from poor body satisfaction, which is traditionallyregarded as a systematic distortion in "body image." In this systematic review,conducted according to the PRISMA statement, the evidence on effectiveness of PI on body representation outcomes is synthesised. We provide an update of 34 longitudinal studies evaluating the effectiveness of different types of PIs on body representation. No systematic risk of bias within or across studies were identified. The reviewed studies show that the implementation of structured PIs may be efficacious in increasing individuals' satisfaction of their own body, and thus improving their subjective body image related assessments. However, there is no clear evidence regarding an additional or interactive effect of PI when implemented in conjunction with established treatments for clinical populations. We argue for theoretically sound, mechanism-oriented, multimethod approaches to future investigations on body image disturbance. Specifically, we highlight the need to consider expanding the theoretical framework for the investigation of body representation disturbances to include further body representations besides body image.
Curated set of cone bipolar cell morphologies for biophysical modelling
2020-03-19

This dataset contains 40 cone bipolar cell morphologies in the .swc file format (skeleton and radius) based on the e2006 EM dataset (Helmstaedter et al., 2013). All morphologies have been manually proof-read. Individual file names consist of the cell ID from the original EM dataset and the cell type following (Behrens et al., 2016).
Implicit? What Do You Mean? A Comprehensive Review of the Delusive Implicitness Construct in Attitude Research
2020-03-20

This article provides a comprehensive review of divergent conceptualizations of the “implicit” construct that have emerged in attitude research over the past two decades. In doing so, our goal is to raise awareness of the harmful consequences of conceptual ambiguities associated with this terminology. We identify three main conceptualizations of the “implicitness” construct: the procedural conceptualization (implicit-as-indirect), the functional conceptualization (implicit-as-automatic), and the mental theory conceptualization (implicit-as-associative), as well as two hybrid conceptualizations (implicit-as-indirect-and-automatic, implicit-as-driven-by-affective-gut-reactions). We discuss critical limitations associated with each conceptualization and explain that confusion also arises from their coexistence. We recommend discontinuing the usage of the “implicit” terminology in attitude research and research inspired by it. We offer terminological alternatives aimed at increasing both the precision of theorization and the practical value of future research.
Effects of an intervention to reduce fear of falling and increase physical activity during hip and pelvic fracture rehabilitation
2020-03-20

Abstract Background fear of falling and reduced fall-related self-efficacy are frequent consequences of falls and associated with poorer rehabilitation outcomes. To address these psychological consequences, geriatric inpatient rehabilitation was augmented with a cognitive behavioural intervention (“Step by Step”) and evaluated in a RCT. Methods one hundred fifteen hip and pelvic fracture patients (age = 82.5 years, 70% female) admitted to geriatric inpatient rehabilitation were randomly allocated to the intervention or control group. The intervention consisted of eight additional individual sessions during inpatient rehabilitation, one home visit and four telephone calls delivered over 2 months after discharge. Both groups received geriatric inpatient rehabilitation. Primary outcomes were fall-related self-efficacy (short falls efficacy scale-international) and physical activity as measured by daily walking duration (activPAL3TM sensor) after admission to rehabilitation, before discharge and 1-month post-intervention. Results in covariance analyses, patients in the intervention group showed a significant improvement in fall-related self-efficacy (P = 0.025, d = −0.42), but no difference in total daily walking duration (P = 0.688, d = 0.07) 1-month post-intervention compared to the control condition. Further significant effects in favour of the intervention group were found in the secondary outcomes “perceived ability to manage falls” (P = 0.031, d = 0.41), “physical performance” (short physical performance battery) (P = 0.002, d = 0.58) and a lower “number of falls” (P = 0.029, d = −0.45). Conclusions the intervention improved psychological and physical performance measures but did not increase daily walking duration. For the inpatient part of the intervention further research on the required minimum intensity needed to be effective is of interest. Duration and components used to improve physical activity after discharge should be reconsidered.
Evidence for Returning Disk Radiation in the Black Hole X-Ray Binary XTE J1550–564
2020-03-20

Abstract We explore the accretion properties of the black hole X-ray binary XTE J1550−564 during its outbursts in 1998/99 and 2000. We model the disk, corona, and reflection components of X-ray spectra taken with the Rossi X-ray Timing Explorer , using the relxill suite of reflection models. The key result of our modeling is that the reflection spectrum in the very soft state is best explained by disk self-irradiation, i.e., photons from the inner disk are bent by the strong gravity of the black hole and reflected off the disk surface. This is the first known detection of thermal disk radiation reflecting off the inner disk. There is also an apparent absorption line at ∼6.9 keV, which may be evidence of an ionized disk wind. The coronal electron temperature ( kT e ) is, as expected, lower in the brighter outburst of 1998/99, explained qualitatively by more efficient coronal cooling due to irradiating disk photons. The disk inner radius is consistent with being within a few times the innermost stable circular orbit throughout the bright-hard-to-soft states (10 s of r g in gravitational units). The disk inclination is low during the hard state, disagreeing with the binary inclination value, and very close to 90° in the soft state, recovering to a lower value when adopting a blackbody spectrum as the irradiating continuum.
Optimal estimation with quantum optomechanical systems in the nonlinear regime
2020-03-20

We study the fundamental bounds on precision measurements of parameters\\ncontained in a time-dependent nonlinear optomechanical Hamiltonian, which\\nincludes the nonlinear light-matter coupling, a mechanical displacement term,\\nand a single-mode mechanical squeezing term. By using a recently developed\\nmethod to solve the dynamics of this system, we derive a general expression for\\nthe quantum Fisher information and demonstrate its applicability through three\\nconcrete examples: estimation of the strength of a nonlinear light-matter\\ncoupling, the strength of a time-modulated mechanical displacement, and a\\nsingle-mode mechanical squeezing parameter, all of which are modulated at\\nresonance. Our results can be used to compute the sensitivity of a nonlinear\\noptomechanical system to a number of external and internal effects, such as\\nforces acting on the system or modulations of the light--matter coupling.\\n
New Nocobactin Derivatives with Antimuscarinic Activity, Terpenibactins A–C, Revealed by Genome Mining of Nocardia terpenica IFM 0406
2020-03-20

Abstract We report a genomics‐guided exploration of the metabolic potential of the brasilicardin producer strain Nocardia terpenica IFM 0406. Bioinformatics analysis of the whole genome sequence revealed the presence of a biosynthetic gene cluster presumably responsible for the generation of formerly unknown nocobactin derivatives. Mass spectrometry‐assisted isolation led to the identification of three new siderophores, terpenibactins A ( 1 ), B ( 2 ) and C ( 3 ), which belong to the class of nocobactins. Their structures were elucidated by employing spectroscopic techniques. Compounds 1 – 3 demonstrated inhibitory activity towards the muscarinic M3 receptor, while exhibiting only a low cytotoxicity.
Standalone cooperation-free OKN-based low vision contrast sensitivity estimation in VR - a pilot study
2020-03-20

The developed OKN-based sensitivity test represents a reliable proof of concept for technology readiness of virtual reality-based screening tools of visual function in practice, specifically in patients with difficulties to report perception verbally, or under conditions, where no experienced examiner is present.
Development of a multivariable prediction model for patient-adjusted aortic risk morphology
2020-03-20

Abstract OBJECTIVES Preventing type A aortic dissection requires reliable prediction. We developed and validated a multivariable prediction model based on anthropometry to define patient-adjusted thresholds for aortic diameter and length. METHODS We analysed computed tomography angiographies and clinical data from 510 control patients, 143 subjects for model validation, 125 individuals with ascending aorta ectasia (45–54 mm), 58 patients with aneurysm (≥55 mm), 206 patients with type A aortic dissection and 19 patients who had received a computed tomography angiography ≤2 years before they suffered from a type A aortic dissection. Computed tomography angiographies were analysed using curved planar reformations. RESULTS In the control group, the mean ascending aortic diameter was 33.8 mm [standard deviation (SD) ±5.2 mm], and the length, measured from the aortic valve to the brachiocephalic trunk, was 91.9 mm (SD ±12.2 mm); both diameter and length were correlated with anthropometric parameters and were smaller than the respective values in all pathological groups (P &amp;lt; 0.001). Multivariable linear regression analysis of the control group revealed that age, sex and body surface area were predictors of ascending aorta diameter (R2 = 0.40) and length (R2 = 0.26). Bicuspidity of the aortic valve was not included in the model; its prevalence was only 3.2% in the control group but &amp;gt;25% in the ectasia and aneurysm groups. CONCLUSIONS The regression model provides a patient-adjusted prediction of the thresholds for aortic diameter and length. In our retrospective data, the model resulted in better identification of aortas at the risk of dissection than the conventional 55-mm diameter threshold. The model is available as an Internet calculator (www.aorticcalculator.com).
The Social Practice of Being Born Again: Historical and Cultural-Sociological Perspectives on Conversionist Piety
2020-03-20

Abstract What kind of practices, emotions and self-understandings are linked to conversion? This contribution offers a set of analytical tools which help to understand processes of constructing, performing and maintaining conversionist identity. In doing so, it builds on both, source material related to 17 th and 18 th century New England and conversion research in the area of sociology, anthropology, and cultural studies. Holistic in its approach, it reconstructs conversionist piety as a social practice that builds up into pious cultures of body, emotion, and meaning-making. The analytical concepts developed on the way may prove to be a starting point for further empirical research on lived religion in Practical Theology and Religious Studies.
New Perspectives for Mucolytic, Anti-inflammatory and Adjunctive Therapy with 1,8-Cineole in COPD and Asthma: Review on the New Therapeutic Approach
2020-03-21

The mucolytic monoterpene 1,8-cineole (eucalyptol), the major constituent of eucalyptus species, is well known for its anti-inflammatory, antioxidant, bronchodilatory, antiviral and antimicrobial effects. The main protective antiviral, anti-inflammatory and mucolytic mechanisms of 1,8-cineole are the induction of interferon regulatory factor 3 (IRF3), the control of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) along with decreasing mucin genes (MUC2, MUC19). In normal human monocytes direct inhibition was shown of reactive oxygen species (ROS)-mediated mucus hypersecretion and of steroid resistence inducing superoxides (O<sub>2</sub><sup>·-</sup>) and pro-inflammatory hydrogen peroxides (H<sub>2</sub>O<sub>2</sub>) with partial control of superoxide dismutase (SOD), which enzymatically metabolizes O<sub>2</sub><sup>·-</sup> into H<sub>2</sub>O<sub>2</sub>. By inhibition of NF-κB, 1,8-cineole, at relevant plasma concentrations (1.5 μg/ml), strongly and significantly inhibited in normal human monocyte lipopolysaccharide (LPS)-stimulated cytokines relevant for exacerbation (tumour necrosis factor alpha (TNFα), interleukin (IL)-1β and systemic inflammation (IL-6, IL-8). Infectious agents and environmental noxa have access via TNFα and IL-1β to the immune system with induction of bronchitis complaints and exacerbations of chronic obstructive pulmonary disease (COPD), asthma and asthma-COPD overlap. In lymphocytes from healthy human donors 1,8-cineole inhibited TNFα, IL-1β, IL-4 and IL-5 and demonstrated for the first time control of Th1/2-type inflammation. 1,8-Cineole at relevant plasma levels increased additively in vitro the efficacy of inhaled guideline medications of budesonide (BUD) and budesonide + formoterol ,and preliminary data also showed increased efficacy of long-acting muscarinic receptor antagonist (LAMA)-mediated cytokine inhibition in vitro. On the basis of the preclinical data, earlier randomised controlled studies with adjunctive therapy of 1,8-cineole (3 × 200 mg/day) for 6 months showed improvement of uncontrolled asthma by significant improvement of lung function, nocturnal asthma and quality of life scores and in COPD decrease of exacerbations (- 38.5%) (during wintertime). This review reports an update with reference to the literature of 1,8-cineole, also as adjunctive therapy, as a therapeutic agent for the protection and control of inflammatory airway diseases.