julilili42/papers huggingface dataset:
The rate and potential relevance of new mutations in a colonizing plant lineage
2018-02-12

By following the evolution of populations that are initially genetically homogeneous, much can be learned about core biological principles. For example, it allows for detailed studies of the rate of emergence of de novo mutations and their change in frequency due to drift and selection. Unfortunately, in multicellular organisms with generation times of months or years, it is difficult to set up and carry out such experiments over many generations. An alternative is provided by "natural evolution experiments" that started from colonizations or invasions of new habitats by selfing lineages. With limited or missing gene flow from other lineages, new mutations and their effects can be easily detected. North America has been colonized in historic times by the plant Arabidopsis thaliana, and although multiple intercrossing lineages are found today, many of the individuals belong to a single lineage, HPG1. To determine in this lineage the rate of substitutions-the subset of mutations that survived natural selection and drift-, we have sequenced genomes from plants collected between 1863 and 2006. We identified 73 modern and 27 herbarium specimens that belonged to HPG1. Using the estimated substitution rate, we infer that the last common HPG1 ancestor lived in the early 17th century, when it was most likely introduced by chance from Europe. Mutations in coding regions are depleted in frequency compared to those in other portions of the genome, consistent with purifying selection. Nevertheless, a handful of mutations is found at high frequency in present-day populations. We link these to detectable phenotypic variance in traits of known ecological importance, life history and growth, which could reflect their adaptive value. Our work showcases how, by applying genomics methods to a combination of modern and historic samples from colonizing lineages, we can directly study new mutations and their potential evolutionary relevance.
Agonistic Autoantibodies to the β2-Adrenergic Receptor Involved in the Pathogenesis of Open-Angle Glaucoma
2018-02-12

Glaucoma is a frequent ocular disease that may lead to blindness. Primary open-angle glaucoma (POAG) and ocular hypertension (OHT) are common diseases with increased intraocular pressure (IOP), which are mainly responsible for these disorders. Their pathogenesis is widely unknown. We screened the sera of patients with POAG and OHT for the prevalence of autoantibodies (AAb) against G protein-coupled receptors (GPCRs) in comparison to controls. Employing frequency modulation of spontaneously contracting neonatal rat cardiomyocytes <i>in vitro</i>, agonistic GPCR AAb were to be detected in roughly 75% of the patients with POAG and OHT, however, not in controls. Using inhibitory peptides the AAb' target was identified as β2 adrenergic receptor (β2AR). The AAb interact with the second extracellular loop of β2AR. The peptides 181-187 and 186-192 were identified as binding sites of the AAb within the extracellular loop II. The binding of the AAb to β2ARs was verified by surface-plasmon-resonance analysis. The isotype of the AAb was (immunoglobulin) IgG3. In an additional pilot principal-of-proof study, including four patients with POAG, the removal of the AAb against the β2AR and other immunoglobulins G by immunoadsorption resulted in a transient reduction of IOP. These findings might indicate a possible role of agonistic AAb directed against β2ARs in the dynamics of aqueous humor and might support a contribution of adaptive autoimmunity in the etiopathogenesis of POAG and OHT.
Tectonic controls of Holocene erosion in a glaciated orogen
2018-02-12

Abstract. Recent work has highlighted a strong, worldwide, glacial impact of orogen erosion rates over the last 2 Ma. While it may be assumed that glaciers increased erosion rates when active, the degree to which past glaciations influence Holocene erosion rates through the adjustment of topography is not known. In this study, we investigate the influence of long-term tectonic and post-glacial topographic controls on erosion in a glaciated orogen, the Olympic Mountains, USA. We present 14 new 10Be and 26Al analyses which constrain Holocene erosion rates across the Olympic Mountains. Basin-averaged erosion rates scale with basin-averaged values of 5-km local relief, channel steepness, and hillslope angle throughout the range, similar to observations from non-glaciated orogens. These erosion rates are not related to mean annual precipitation or the marked change in Pleistocene alpine glacier size across the range, implying that glacier modification of topography and modern precipitation parameters do not exert strong controls on these rates. Rather, we find that despite intense spatial variations in glacial modification of topography, patterns of recent erosion are similar to those from estimates of long-term tectonic rock uplift. This is consistent with a tectonic model where erosion and rock uplift patterns are controlled by the deformation of the Cascadia subduction zone.
Problems in anticoagulation of a patient with antibiotic treatment for endocarditis: interaction of rifampicin and vitamin K antagonists
2018-02-12

The cytochrome P450 is a superfamily of isoenzymes that are responsible for the metabolism of many drugs. Significant changes in pharmacokinetics and drug interactions may be due to induction of hepatic cytochrome P450 enzymes. Rifampicin is a common inducer of CYP3A4. We report a case of a 57-year-old woman who was suspected for endocarditis and therefore treated with rifampicin. Due to previous mechanical aortic valve replacement, she also received phenprocoumon for anticoagulation. Although continuing anticoagulant therapy, antibiotic coadministration led to normal international normalised ratio (INR) level. Fifteen days after the treatment with rifampicin ended, INR returned to therapeutic level.
A Unified Method for Placing Problems in Polylogarithmic Depth
2018-02-12

In this work we consider the term evaluation problem which is, given a term over some algebra and a valid input to the term, computing the value of the term on that input. In contrast to previous methods we allow the algebra to be completely general and consider the problem of obtaining an efficient upper bound for this problem. Many variants of the problems where the algebra is well behaved have been studied. For example, the problem over the Boolean semiring or over the semiring (N,+,*). We extend this line of work. Our efficient term evaluation algorithm then serves as a tool for obtaining polylogarithmic depth upper bounds for various well-studied problems. To demonstrate the utility of our result we show new bounds and reprove known results for a large spectrum of problems. In particular, the applications of the algorithm we consider include (but are not restricted to) arithmetic formula evaluation, word problems for tree and visibly pushdown automata, and various problems related to bounded tree-width and clique-width graphs.
LytM factor Alr3353 affects filament morphology and cell–cell communication in the multicellular cyanobacterium Anabaena sp. PCC 7120
2018-02-13

Summary Heterocyst‐forming cyanobacteria are organized as multicellular filaments of tightly interacting, functionally specialized cells. N 2 ‐fixing heterocysts differentiate from vegetative cells under nitrogen limitation in a semi‐regular pattern along the filament. Diazotrophic growth requires metabolite exchange between neighboring cells within the filament. This exchange occurs via cell–cell junction complexes that span the gap between the plasma membranes and thereby cross the septal peptidoglycan through an array of uniform nanopores formed by AmiC‐type cell wall hydrolases. We investigated how the lytic hydrolase AmiC1 (Alr0092) from Anabaena sp. PCC 7120, whose activity needs to be tightly controlled to avoid cell lysis, is regulated by the LytM factor Alr3353. Inactivation of alr3353 resulted in significantly fewer nanopores and as a consequence, a lower rate of fluorescent tracer exchange between cells. The mutant was not able to grow with N 2 as sole nitrogen source, although heterocysts were formed. Alr3353 localized mainly to fully developed intercellular septa of vegetative cells. The purified protein bound to peptidoglycan and enhanced the hydrolytic activity of AmiC1 in vitro . Our data show that the LytM factor Alr3353 regulates nanopore formation and cell–cell communication by directly interacting with AmiC1.
Inverse spectrum problem for quasi-stationary states
2018-02-13

In this work we present a semi-classical approach to solve the inverse\\nspectrum problem for one-dimensional wave equations for a specific class of\\npotentials that admits quasi-stationary states. We show how inverse methods for\\npotential wells and potential barriers can be generalized to reconstruct\\nsignificant parts for the combined potentials. For the reconstruction one\\nassumes the knowledge of the complex valued spectrum and uses the exponential\\nsmallness of its imaginary part. Analytic spectra are studied and a recent\\napplication of the method in the literature for gravitational wave physics is\\ndiscussed. The method allows for a simple reconstruction of quasi-stationary\\nstate potentials from a given spectrum. Thus it might be interesting for\\ndifferent branches of physics and related fields.\\n
Anion dependent ion pairing in concentrated ytterbium halide solutions
2018-02-13

We have studied ion pairing of ytterbium halide solutions. THz spectra (30-400 cm−1) of aqueous YbCl3 and YbBr3 solutions reveal fundamental differences in the hydration structures of YbCl3 and YbBr3 at high salt concentrations: While for YbBr3 no indications for a changing local hydration environment of the ions were experimentally observed within the measured concentration range, the spectra of YbCl3 pointed towards formation of weak contact ion pairs. The proposed anion specificity for ion pairing was confirmed by supplementary Raman measurements.
FISH PREDATION ON A MEDITERRANEAN ECHINOID: IDENTIFICATION AND PRESERVATION POTENTIAL
2018-02-13

Research Article| February 13, 2018 FISH PREDATION ON A MEDITERRANEAN ECHINOID: IDENTIFICATION AND PRESERVATION POTENTIAL DIEDRICH SIEVERS; DIEDRICH SIEVERS Universität Tübingen, Fachbereich Geowissenschaften, Hölderlinstr. 12, 72074 Tübingen, Germany Search for other works by this author on: GSW Google Scholar JAMES H. NEBELSICK JAMES H. NEBELSICK Universität Tübingen, Fachbereich Geowissenschaften, Hölderlinstr. 12, 72074 Tübingen, Germany Search for other works by this author on: GSW Google Scholar Author and Article Information DIEDRICH SIEVERS Universität Tübingen, Fachbereich Geowissenschaften, Hölderlinstr. 12, 72074 Tübingen, Germany JAMES H. NEBELSICK Universität Tübingen, Fachbereich Geowissenschaften, Hölderlinstr. 12, 72074 Tübingen, Germany email: diedrich_sievers@web.de Publisher: SEPM Society for Sedimentary Geology First Online: 13 Feb 2018 Online Issn: 1938-5323 Print Issn: 0883-1351 Copyright © 2018, SEPM (Society for Sedimentary Geology) PALAIOS (2018) 33 (2): 47–54. https://doi.org/10.2110/palo.2017.041 Article history First Online: 13 Feb 2018 Cite View This Citation Add to Citation Manager Share Icon Share Facebook Twitter LinkedIn MailTo Tools Icon Tools Get Permissions Search Site Citation DIEDRICH SIEVERS, JAMES H. NEBELSICK; FISH PREDATION ON A MEDITERRANEAN ECHINOID: IDENTIFICATION AND PRESERVATION POTENTIAL. PALAIOS 2018;; 33 (2): 47–54. doi: https://doi.org/10.2110/palo.2017.041 Download citation file: Ris (Zotero) Refmanager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentBy SocietyPALAIOS Search Advanced Search Abstract Wound morphologies on the Recent Mediterranean echinoid Sphaerechinus granularis (Lamarck) from the Italian island of Giglio allow the reconstruction of predation events by sparid fish. These lethal attacks leave characteristic bite marks and other features including scratch marks of teeth, bitten off spines, and fragmented jaw supports. The bite marks consist of semicircular indentation on the edge of a gaping wound showing intraplate fragmentation. The attack is initiated on the upper side of the echinoid test. Comparison of predation traces to jaw and tooth morphologies allows the sparid fish Diplodus vulgaris (Geoffroy Saint-Hillaire) and Diplodus sargus (L.) to be identified as the most likely predators. This type of fish predation is compared to other known predatory attacks on echinoid taxa in the Mediterranean Sea. The fossilization potential of this type of predation is discussed with respect to test preservation, based on the degree of fragmentation, abrasion and encrustation of the individual tests, and the specific habitat in which these echinoids are found. You do not have access to this content, please speak to your institutional administrator if you feel you should have access.
Population study of Galactic supernova remnants at very highγ-ray energies with H.E.S.S.
2018-02-14

Shell-type supernova remnants (SNRs) are considered prime candidates for the acceleration of Galactic cosmic rays (CRs) up to the knee of the CR spectrum at E ≈ 3 × 10 15 eV. Our Milky Way galaxy hosts more than 350 SNRs discovered at radio wavelengths and at high energies, of which 220 fall into the H.E.S.S. Galactic Plane Survey (HGPS) region. Of those, only 50 SNRs are coincident with a H.E.S.S source and in 8 cases the very high-energy (VHE) emission is firmly identified as an SNR. The H.E.S.S. GPS provides us with a legacy for SNR population study in VHE γ -rays and we use this rich data set to extract VHE flux upper limits from all undetected SNRs. Overall, the derived flux upper limits are not in contradiction with the canonical CR paradigm. Assuming this paradigm holds true, we can constrain typical ambient density values around shell-type SNRs to n ≤ 7 cm −3 and electron-to-proton energy fractions above 10 TeV to ε ep ≤ 5 × 10 −3 . Furthermore, comparisons of VHE with radio luminosities in non-interacting SNRs reveal a behaviour that is in agreement with the theory of magnetic field amplification at shell-type SNRs.
Approaching adaptive control in neurostimulation for Parkinson disease
2018-02-14

Tailoring therapy for the patient's individual motor state and daily life requirements is a long-standing vision in Parkinson disease (PD) treatment. This is particularly true when motor fluctuations emerge as a major impairment. Subthalamic nucleus deep brain stimulation (DBS) attenuates motor fluctuations and improves quality of life in PD.1,2 However, it is still delivered in a rather rigid way, with mostly constant stimulation parameters between patient visits and physician reprogramming sessions.
Periaortic Adipose Tissue Compared With Peribrachial Adipose Tissue Mass as Markers and Possible Modulators of Cardiometabolic Risk
2018-02-14

Increased perivascular fat mass contributes to cardiometabolic risk (CMR). High peribrachial adipose tissue (PBAT) associates with insulin resistance independently of established CMR parameters. It is unknown to what extent periaortic adipose tissue (PAAT) may have a similar impact. In 95 participants, precise quantification of total adipose tissue, PBAT, PAAT, visceral adipose tissue (VAT), and liver fat (LF) content was performed by whole-body magnetic resonance imaging. Insulin sensitivity was determined by oral glucose tolerance test and carotid intima–media thickness (cIMT) by high-resolution ultrasound. In univariate analyses, PAAT correlated with PBAT (β = .65, P &lt; .0001). A negative correlation of PAAT (β = −.35, P = .0002) and PBAT (β = −.43, P &lt; .0001) with insulin sensitivity was observed. While in a stepwise forward regression analysis the relationship of PAAT with insulin sensitivity was no longer significant after adjustment for VAT, LF content, and other CMR factors ( P = 0.42), PBAT still correlated with insulin sensitivity ( r 2 = .35, P = .01). The association between PAAT and cIMT (β = .49, P &lt; .0001) remained significant after adjustment for these variables ( r 2 = .42, P = .0001). Although PAAT and PBAT strongly correlate, PAAT is not associated with insulin resistance, but with cIMT. Therefore, PAAT and PBAT may act differently as possible modulators of insulin resistance and subclinical atherosclerosis.
Quantitative Imaging and Imaging Biomarkers
2018-02-14

Department of Diagnostic and Interventional Radiology, University of Tübingen, Tübingen, Germany Supported by Siemens Healthcare (Forchheim, Germany), Bayer Healthcare (Berlin, Germany). F.B.: speaker’s bureau, Siemens Healthcare (Forchheim, Germany), Bayer Healthcare (Berlin, Germany). Correspondence to: Fabian Bamberg, MD, MPH, Department of Diagnostic and Interventional Radiology, University of Tübingen, Hoppe-Seyler-Straße 3, Tübingen 72076, Germany (e-mail: [email protected]).
The Draft Provisions on Antitrust Fines in the Commission's Ecn Proposal
2018-02-14

With its Proposal for a directive to empower the competition authorities of the Member States to be more effective enforcers (“ECN Proposal”), the Commission has undertaken great effort to harmonise public enforcement throughout the Member States and has thereby entered uncharted waters. With this article, the authors intend to take a closer look at two major pillars of the ECN Proposal: the introduction of the Commission’s economic entity doctrine to national antitrust laws as well as the aspired harmonisation of the Member States’ leniency programmes. The authors are sceptical towards the idea of the economic entity doctrine becoming the unitary sanctioning concept throughout the EU. Also, they argue that the introduction of a 10% fine cap for any National Competition Authority irrespective of the size of the Member State can lead to highly disparate relative fining powers throughout the internal market. As to the leniency aspect, the present article elaborates on a one-stop-shop leniency principle. Such would go beyond the current Proposal in that it would render multiple leniency filings obsolete within the EU.
A multiscale modelling approach to assess the impact of metabolic zonation and microperfusion on the hepatic carbohydrate metabolism
2018-02-15

The capacity of the liver to convert the metabolic input received from the incoming portal and arterial blood into the metabolic output of the outgoing venous blood has three major determinants: The intra-hepatic blood flow, the transport of metabolites between blood vessels (sinusoids) and hepatocytes and the metabolic capacity of hepatocytes. These determinants are not constant across the organ: Even in the normal organ, but much more pronounced in the fibrotic and cirrhotic liver, regional variability of the capillary blood pressure, tissue architecture and the expression level of metabolic enzymes (zonation) have been reported. Understanding how this variability may affect the regional metabolic capacity of the liver is important for the interpretation of functional liver tests and planning of pharmacological and surgical interventions. Here we present a mathematical model of the sinusoidal tissue unit (STU) that is composed of a single sinusoid surrounded by the space of Disse and a monolayer of hepatocytes. The total metabolic output of the liver (arterio-venous glucose difference) is obtained by integration across the metabolic output of a representative number of STUs. Application of the model to the hepatic glucose metabolism provided the following insights: (i) At portal glucose concentrations between 6-8 mM, an intra-sinusoidal glucose cycle may occur which is constituted by glucose producing periportal hepatocytes and glucose consuming pericentral hepatocytes, (ii) Regional variability of hepatic blood flow is higher than the corresponding regional variability of the metabolic output, (iii) a spatially resolved metabolic functiogram of the liver is constructed. Variations of tissue parameters are equally important as variations of enzyme activities for the control of the arterio-venous glucose difference.
Ultraluminous X-ray sources as neutrino pulsars
2018-02-15

The classical limit on the accretion luminosity of a neutron star is given by the Eddington luminosity. The advanced models of accretion on to magnetized neutron stars account for the appearance of magnetically confined accretion columns and allow the accretion luminosity to be higher than the Eddington value by a factor of tens. However, the recent discovery of pulsations from ultraluminous X-ray source (ULX) in NGC 5907 demonstrates that the accretion luminosity can exceed the Eddington value up to by a factor of 500. We propose a model explaining observational properties of ULX-1 in NGC 5907 without any ad hoc assumptions. We show that the accretion column at extreme luminosity becomes advective. Enormous energy release within a small geometrical volume and advection result in very high temperatures at the bottom of accretion column, which demand to account for the energy losses due to neutrino emission which can be even more effective than the radiation energy losses. We show that the total luminosity at the mass accretion rates above 1021 g s-1 is dominated by the neutrino emission similarly to the case of core-collapse supernovae. We argue that the accretion rate measurements based on detected photon luminosity in case of bright ULXs powered by neutron stars can be largely underestimated due to intense neutrino emission. The recently discovered pulsating ULX-1 in galaxy NGC 5907 with photon luminosity of { ̃ } 10^{41} {erg s^{-1}} is expected to be even brighter in neutrinos and is thus the first known Neutrino Pulsar.
Drp1 polymerization stabilizes curved tubular membranes similar to those of constricted mitochondria
2018-02-15

ABSTRACT Dynamin-related protein 1 (Drp1), an 80 kDa mechanochemical GTPase of the dynamin superfamily, is required for mitochondrial division in mammals. Despite the role of Drp1 dysfunction in human disease, its molecular mechanism remains poorly understood. Here, we examined the effect of Drp1 on membrane curvature using tubes pulled from giant unilamellar vesicles (GUVs). We found that GTP promoted rapid rearrangement of Drp1 from a uniform distribution to discrete foci, in line with the assembly of Drp1 scaffolds at multiple nucleation sites around the lipid tube. Polymerized Drp1 preserved the membrane tube below the protein coat, also in the absence of pulling forces, but did not induce spontaneous membrane fission. Strikingly, Drp1 polymers stabilized membrane curvatures similar to those of constricted mitochondria against pressure changes. Our findings support a new model for mitochondrial division whereby Drp1 mainly acts as a scaffold for membrane curvature stabilization, which sets it apart from other dynamin homologs.
Ge14Br8(PEt3)4: A Subhalide Cluster of Germanium
2018-02-15

Abstract Heating a metastable solution of Ge I Br to room temperature led to the first structurally characterized metalloid subhalide cluster Ge 14 Br 8 (PEt 3 ) 4 ( 1 ). Furthermore 1 can be seen as the first isolated binary halide cluster on the way from Ge I Br to elemental germanium, giving insight into the complex reaction mechanism of its disproportionation reaction. Quantum chemical calculations further indicate that a classical bonding situation is realized within 1 and that the last step of the formation of 1 might include the trapping of GeBr 2 units.