julilili42/papers huggingface dataset:
Ancestral state reconstruction and loanword detection
2016-03-02

Building on established applications of methods from bioinformatics to historical linguistics, we investigate the potential of different ancestral state reconstruction (ASR) methods for the task of loanword detection. Based on a very simple criterion for deriving loanword judgments from reconstructed ancestral states, we compare the performance of two state-ofthe-art approaches to ASR against a very simple thresholdbased, more linguistically motivated reconstruction method. We evaluate on the Indo-European cognacy judgments encoded in the IELex database. While overall performance is very low due to the properties of the dataset, there are marked differences in precision between the three methods, demonstrating that the development of specialized reconstruction methods for computational historical linguistics is worth pursuing.
Divergence Times and Phylogenetic Patterns of Sebacinales, a Highly Diverse and Widespread Fungal Lineage
2016-03-03

Patterns of geographic distribution and composition of fungal communities are still poorly understood. Widespread occurrence in terrestrial ecosystems and the unique richness of interactions of Sebacinales with plants make them a target group to study evolutionary events in the light of nutritional lifestyle. We inferred diversity patterns, phylogenetic structures and divergence times of Sebacinales with respect to their nutritional lifestyles by integrating data from fossil-calibrated phylogenetic analyses. Relaxed molecular clock analyses indicated that Sebacinales originated late Permian within Basidiomycota, and their split into Sebacinaceae and Serendipitaceae nom. prov. likely occurred during the late Jurassic and the early Cretaceous, coinciding with major diversifications of land plants. In Sebacinaceae, diversification of species with ectomycorrhizal lifestyle presumably started during the Paleocene. Lineage radiations of the core group of ericoid and cavendishioid mycorrhizal Sebacinales started probably in the Eocene, coinciding with diversification events of their hosts. The diversification of Sebacinales with jungermannioid interactions started during the Oligocene, and occurred much later than the diversification of their hosts. Sebacinales communities associated either with ectomycorrhizal plants, achlorophyllous orchids, ericoid and cavendishioid Ericaceae or liverworts were phylogenetically clustered and globally distributed. Major Sebacinales lineage diversifications started after the continents had drifted apart. We also briefly discuss dispersal patterns of extant Sebacinales.
Forming associations between language and sensorimotor traces during novel word learning
2016-03-03

abstract Embodied models of language comprehension are based on the assumption that words become associated with sensorimotor experiences during initial word learning. To test this hypothesis, adult participants learned artificial words as labels for novel objects in a multisensory environment. In a word learning phase, novel objects were located in the participant’s upper or lower visual field and participants learned the objects’ names by interacting with them. In a test phase, participants responded to the color of the words with either an upwards or a downwards directed arm movement in a Stroop-like paradigm. Responses were fastest when the movement direction was compatible with the word’s referent location (i.e., the location of the novel object in vertical space) during the learning phase. This finding suggests that sensorimotor experiences become associated with words during initial word learning. The results of the current study and implications for language learning are discussed.
An Attitude Strength and Self-Perception Framework Regarding the Bi-directional Relationship of Job Satisfaction with Extra-Role and In-Role Behavior: The Doubly Moderating Role of Work Centrality
2016-03-03

Studies have identified variables either moderating the extent to which job satisfaction predicts work behavior or moderating the reverse impact of work behavior on job satisfaction. Based on an attitude strength and self-perception framework, we argue that certain variables may moderate both the predictive utility of job satisfaction for work behavior and the impact of work behavior on job satisfaction. Specifically focusing on work centrality, we hold that high work centrality renders job satisfaction a strong job attitude, whereas low work centrality renders job satisfaction a weak job attitude. Hence, the predictive utility of job satisfaction for both extra-role behavior and in-role behavior should be higher the more work is central to employees. In contrast, the influence of extra-role behavior, but not of in-role behavior, on job satisfaction should be higher the less work is central to employees. Results of a two-wave study (N = 176) were in line with these predictions. We discuss further variables that may play a similar role for the bi-directional relationship between job satisfaction and work behavior.
Evidence for an evolving cyclotron line energy in 4U 1538−522
2016-03-03

We have performed a full time and luminosity-resolved spectral analysis of the high-mass X-ray binary 4U 1538−522 using the available &lt;it&gt;RXTE, INTEGRAL&lt;/it&gt;, and &lt;it&gt;Suzaku&lt;/it&gt; data, examining both phase-averaged and pulse-phase-constrained data sets and focusing on the behaviour of the cyclotron resonance scattering feature (CRSF). No statistically significant trend between the energy of the CRSF and luminosity is observed in the combined data set. However, the CRSF energy appears to have increased by ∼1.5 keV in the ∼8.5 yr between the &lt;it&gt;RXTE&lt;/it&gt; and &lt;it&gt;Suzaku&lt;/it&gt; measurements, with Monte Carlo simulations finding the &lt;it&gt;Suzaku&lt;/it&gt; measurement 4.6σ above the &lt;it&gt;RXTE&lt;/it&gt; points. Interestingly, the increased &lt;it&gt;Suzaku&lt;/it&gt; CRSF energy is much more significant and robust in the pulse-phase-constrained spectra from the peak of the main pulse, suggesting a change that is limited to a single magnetic pole. The seven years of &lt;it&gt;RXTE&lt;/it&gt; measurements do not show any strongly significant evolution with time on their own. We discuss the significance of the CRSF's behaviour with respect to luminosity and time in the context of historical observations of this source as well as recent observational and theoretical work concerning the neutron star accretion column, and suggest some mechanisms by which the observed change over time could occur.
Enhanced Stability of Rubrene against Oxidation by Partial and Complete Fluorination
2016-03-03

We report on the oxidation potential of partially fluorinated (C42F14H14, F14-RUB) and perfluorinated rubrene (C42F28, PF-RUB) studied by cyclic voltammetry (CV) in solution as well as by spectroscopic ellipsometry and near edge X-ray absorption fine structure (NEXAFS) spectroscopy in thin films in combination with density functional theory computations. Due to their different electronic structure, the fluorinated derivatives have a higher oxidation potential and are more stable than rubrene (C42H28, RUB).
Cardiomyocyte generation from somatic sources — current status and future directions
2016-03-03

Transdifferentiation of one cell type to another has garnered significant research efforts in recent years. As cardiomyocyte loss following myocardial infarction becomes debilitating for cardiac patients, the option of an autologous source of cardiomyocytes not derived from multi/pluripotent stem cell sources is an attractive option. Such direct programming has been clearly realized with the use of transcription factors, microRNAs and more recently small molecule delivery to enhance epigenetic modifications, all albeit with low efficiencies in vitro. In this review, we aim to present a brief overview of the current in vitro and in vivo transdifferentiation strategies in the generation of cardiomyocytes from somatic sources. The interdisciplinary fields of tissue, cell, material and regenerative engineering offer many opportunities to synergistically achieve directly programmed cardiac tissue in vitro and enhance transdifferentiation in vivo. This review aims to present a concise outlook on this topic with these fields in mind.
Using computational criteria to extract large Swadesh lists for lexicostatistics
2016-03-03

We propose a new method for empirically determining lists of basic concepts for the purpose of compiling extensive lexicostatistical databases. The idea is to approximate a notion of “swadeshness” formally and reproducibly without expert knowledge or bias, and being able to rank any number of concepts given enough data. Unlike previous approaches, our procedure indirectly measures both stability of concepts against lexical replacement, and their proneness to phenomena such as onomatopoesia and extensive borrowing. The method provides a fully automated way to generate customized Swadesh lists of any desired length, possibly adapted to a given geographical region. We apply the method to a large lexical database of Northern Eurasia, deriving a swadeshness ranking for more than 5,000 concepts expressed by German lemmas. We evaluate this ranking against existing shorter lists of basic concepts to validate the method, and give an English version of the 300 top concepts according to this ranking.
Investigating the potential of ancestral state reconstruction algorithms in historical linguistics
2016-03-03

Current efforts in computational historical linguistics are predominantly concerned with phylogenetic inference. However, methods for ancestral state reconstruction have been only sporadically applied. This is surprising since reconstruction is considered essential both in evolutionary biology and in classical historical linguistics. In contradistinction to phylogenetic algorithms, automatic reconstruction methods presuppose phylogenetic information in order to explain what has evolved when and where. Here we report a pilot study on the potential of reconstruction algorithms in historical linguistics. Based on an explicit family tree, we apply different algorithms to wordlist data in order to infer how the words evolved along the phylogeny, and which words were used without change of meaning in the ancestral languages.
Functional neuroimaging studies in functional dyspepsia patients: a systematic review
2016-03-04

Abstract Background There is increasing evidence in support of the presence of abnormal central changes (compared to healthy controls) in functional dyspepsia ( FD ) in addition to the peripheral changes in gastrointestinal tract. Purpose This systematic review aims to provide an integrative understanding of the abnormal functional brain activity, visceral sensation, dyspeptic symptoms, and psychological changes of FD . Electronic and hand searches were conducted to identify functional neuroimaging studies involving FD patients. Sixteen studies were selected and divided into three categories: 10 resting state studies, three visceral distention studies, and three acupuncture studies. Changes were reported in several brain areas in FD patients including the frontal cortex, somatosensory cortex, insula, anterior cingulate cortex, thalamus, hippocampus, and amygdala. These brain activity changes were associated with visceral hypersensitivity, dyspeptic symptoms, poorer quality of life, anxiety, and depression. The results show that FD is associated with functional abnormalities in sensory and pain modulation, emotion, saliency, and homeostatic processing regions. The diversity of conditions, heterogeneous results, poorly standardized diagnoses of FD , and various comorbidities may be responsible for the variability in the results.
Internet Searching About Disease Elicits a Positive Perception of Own Health When Severity of Illness Is High: A Longitudinal Questionnaire Study
2016-03-04

The results of this study suggest that patients might process information from the Internet selectively, in an unbalanced, biased fashion, with the formation of a self-serving (ie, positive) perception of own health. At the same time, this bias contributes to the ability of patients to cope psychologically with their disease.
Normal Values for the Full Visual Field, Corrected for Age- and Reaction Time, Using Semiautomated Kinetic Testing on the Octopus 900 Perimeter
2016-03-04

A description of the entire kinetic VF is useful for assessing a full characterization of VF sensitivity, determining function losses associated with ocular and neurologic diseases, and for providing a more comprehensive analysis of structure-function relationships.
Proteomic Profiling Suggests Central Role Of STAT Signaling during Retinal Degeneration in the rd10 Mouse Model
2016-03-04

The rd10 mouse is a model of retinitis pigmentosa characterized by the dysfunction of a rod-photoreceptor-specific phosphodiesterase. Compared to the rd1 mouse, retinal degeneration in the rd10 mouse begins later in age with a milder phenotype, making it ideal for investigating cell death and neuroprotective mechanisms. Alterations in the rd10 retina proteome at pre-, peak-, and postdegenerative time points were examined using a modified high-recovery filter-aided sample preparation (FASP) method in combination with label-free quantitative mass spectrometry, generating a proteomic data set on almost 3000 proteins. Our data confirmed a period of protein expression similar to age-matched wild-type mice predegeneration, with decreases in proteins associated with phototransduction and increases in signaling proteins at peak- and postdegenerative stages. A total of 57 proteins were differentially expressed in the rd10 retinae during peak-degeneration, compared to those in wild-type mice after stringent FDR correction (q < 0.05). Network analysis separated these proteins into one cluster of down-regulated photoreceptor proteins and one of up-regulated signaling proteins centered around GFAP, STAT3, and STAT1. This is the first study to identify alterations in STAT1 in the rd10 mouse, which were confirmed with gene expression and immunoblotting experiments, underpinning the efficacy of our approach. This unique proteomic data set on protein dynamics during retinal degeneration could serve as an information source for vision research in the future.
Just Imagine! Learning to Emulate and Infer Actions with a Stochastic Generative Architecture
2016-03-04

Theories on embodied cognition emphasize that our mind develops by processing and inferring structures given the encountered bodily experiences. Here we propose a distributed neural network architecture that learns a stochastic generative model from experiencing bodily actions. Our modular system learns from various manifolds of action perceptions in the form of (i) relative positional motion of the individual body parts, (ii) angular motion of joints, as well as (iii) relatively stable top-down action identities. By Hebbian learning, this information is spatially segmented in separate neural modules that provide embodied state codes as well as temporal predictions of the state progression inside and across the modules. The network is generative in space and time, thus, being able to predict both, missing sensory information as well as next sensory information. We link the developing encodings to visuo-motor and multimodal representations that appear to be involved in action observation. Our results show that the system learns to infer action types as well as motor codes from partial sensory information by emulating observed actions with the own developing body model. We further evaluate the generative capabilities by showing that the system is able to generate internal imaginations of the learned types of actions without sensory stimulation, including visual images of the actions. The model highlights the important roles of motor cognition and embodied simulation for bootstrapping action understanding capabilities. We conclude that stochastic generative models appear very suitable for both, generating goal-directed actions, as well as predicting observed visuo-motor trajectories and action goals.
Next-to-leading order QCD corrections to associated production of a SM Higgs boson with a pair of weak bosons in the POWHEG-BOX
2016-03-04

After the discovery of a Higgs boson in 2012 at the CERN Large Hadron Collider (LHC) the detailed study of its properties, and most importantly its couplings to other particles, has started. This is a very important task to be completed, in particular to test whether it is indeed the Higgs boson predicted by the Standard Model (SM). The precise study of the Higgs couplings to gauge bosons is of particular importance and requires as much information as possible. In this view this paper provides the next-to-leading order (NLO) QCD corrections to the production cross sections and differential distributions of a SM Higgs boson in association with a pair of weak bosons , and , matched with parton shower (PS) in the POWHEG-BOX framework. The NLO QCD corrections are found to be significant and PS effects are sizable at low in the jet differential distributions, as expected, while these effects are negligible in other distributions. We will also provide a detailed study of the theoretical uncertainties affecting the total production rates at the LHC and at the Future Circular Collider in hadron-hadron mode, the potential 100 TeV follow-up of the LHC machine: the scale uncertainty calculated by the variation of the renormalization and factorization scales, the parton distribution function and related errors as well as the parametric uncertainties on the input weak boson masses.
Added Value of Long-Term Cytokine Release Assays to Detect Mycobacterium tuberculosis Infection in HIV-Infected Subjects in Uganda
2016-03-04

Objectives: To investigate whether mycobacterial antigen–induced cytokine secretions are helpful in detecting Mycobacterium tuberculosis ( Mtb ) infection in a cohort of HIV-infected patients living in a country with a high burden of Mtb and HIV infections, and to determine their predictive value for the development of tuberculosis (TB)-associated immune reconstitution inflammatory syndrome. Design: A total of 352 HIV-infected patients (186 with active TB) were prospectively enrolled when initiating antiretroviral therapy (ART). Sequential blood samples were collected during the first 6 months of ART. Eighty-three HIV-uninfected subjects (39 with active TB) were enrolled as controls. Methods: The concentrations of 13 cytokines were measured in supernatants from blood mononuclear cells in vitro stimulated with purified protein derivative (PPD), heparin-binding hemagglutinin (HBHA) or early secreted antigen-6 (ESAT-6) and culture filtrate protein-10 (CFP-10), and results were compared with those of tuberculin skin tests (TST). Results: The best detection of Mtb infection was achieved by ESAT-6/CFP-10–induced interferon-γ concentrations, but results were often negative for patients with CD4 + T-cell counts &lt;50 per cubic millimeters. Patients with active TB were identified by high ESAT-6/CFP-10–induced interleukin-6. Conversions of interferon-γ-release assays (IGRA) and TST occurred under ART, and combined TB and antiretroviral treatments of coinfected patients resulted in a decrease of ESAT-6/CFP-10–induced and an increase of HBHA-induced interferon-γ responses. No Mtb antigen–induced cytokines allowed us to predict TB–immune reconstitution inflammatory syndrome or ART-associated TB. Conclusions: In Uganda, ESAT-6/CFP-10–IGRA is better in detecting Mtb infection than TST and, when combined with an HBHA–IGRA, could help to evaluate anti-TB treatment success.
Challenges in Large-Scale Computational Mass Spectrometry and Multiomics
2016-03-04

ADVERTISEMENT RETURN TO ISSUEEditorialNEXTChallenges in Large-Scale Computational Mass Spectrometry and MultiomicsOliver Kohlbacher*, Olga Vitek*, and Susan T. Weintraub*View Author Information Center for Bioinformatics, Quantitative Biology Center, Department of Computer Science and Faculty of Medicine, University of Tübingen and Max Planck Institute for Developmental Biology Sy and Laurie Sternberg Interdisciplinary Associate Professor, College of Science College of Computer and Information Science, Northeastern University Department of Biochemistry, The University of Texas Health Science Center at San Antonio*O.K.: E-mail: [email protected]. Tel: +49 7071 29 70458.*O.V.: E-mail: [email protected]. Tel: +1 765-409-0172.*S.T.W.: E-mail: [email protected]. Tel: +1 210-567-4043.Cite this: J. Proteome Res. 2016, 15, 3, 681–682Publication Date (Web):March 4, 2016Publication History Published online4 March 2016Published inissue 4 March 2016https://pubs.acs.org/doi/10.1021/acs.jproteome.6b00067https://doi.org/10.1021/acs.jproteome.6b00067editorialACS PublicationsCopyright © 2016 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views1842Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (138 KB) Get e-AlertscloseSUBJECTS:Cancer,Computational chemistry,Genomics,Peptides and proteins,Proteomics Get e-Alerts
Phosphatidylcholine kinetics in neonatal rat lungs and the effects of rhuKGF and betamethasone
2016-03-05

Surfactant, synthesized by type II pneumocytes (PN-II), mainly comprises phosphatidylcholine (PC) and is essential to prevent neonatal respiratory distress. Furthermore, PC is essential to lung tissue growth and maintenance as a membrane component. Recent findings suggest that the lung contributes to systemic lipid homeostasis via PC export through ABC-A1 transporter expression. Hence it is important to consider pharmacological interventions in neonatal lung PC metabolism with respect to such export. Five-day-old rats were treated with carrier (control), intraperitoneal betamethasone, subcutaneous recombinant human keratinocyte growth factor (rhuKGF), or their combination for 48 h. Animals were intraperitoneally injected with 50 mg/kg [D 9 -methyl]choline chloride 1.5, 3.0, and 6.0 h before death at day 7, and lung lavage fluid (LLF) and tissue were harvested. Endogenous PC, D 9 -labeled PC species, and their water-soluble precursors (D 9 -)choline and (D 9 -)phosphocholine were determined by tandem mass spectrometry. Treatment increased secreted and tissue PC pools but did not change equilibrium composition of PC species in LLF. However, all treatments increased specific surfactant components in tissue. In control rats, peak D 9 -PC in lavaged lung was reached after 3 h and was decreased at 6 h. Only 13% of this net loss in lavaged lung was found in LLF. Such decrease was not present in lungs treated with betamethasone and/or with rhuKGF. D 9 -PC loss at 3–6 h and PC synthesis calculated from D 9 enrichment of phosphocholine indicated that daily synthesis rate is higher than total pool size. We conclude that lung tissue contributes to systemic PC homeostasis in neonatal rats, which is altered by glucocorticoid and rhuKGF treatment.