julilili42/papers huggingface dataset:
Structure-Activity Relationship of Chlorotoxin-Like Peptides
2016-02-02

Animal venom (e.g., scorpion) is a rich source of various protein and peptide toxins with diverse physio-/pharmaco-logical activities, which generally exert their action via target-specific modulation of different ion channel functions. Scorpion venoms are among the most widely-known source of peptidyl neurotoxins used for callipering different ion channels, such as; Na+, K+, Ca+, Cl−, etc. A new peptide of the chlorotoxin family (i.e., Bs-Tx7) has been isolated, sequenced and synthesized from scorpion Buthus sindicus (family Buthidae) venom. This peptide demonstrates 66% with chlorotoxin (ClTx) and 82% with CFTR channel inhibitor (GaTx1) sequence identities reported from Leiurus quinquestriatus hebraeus venom. The toxin has a molecular mass of 3821 Da and possesses four intra-chain disulphide bonds. Amino acid sequence analysis of Bs-Tx7 revealed the presence of a scissile peptide bond (i.e., Gly-Ile) for human MMP2, whose activity is increased in the case of tumour malignancy. The effect of hMMP2 on Bs-Tx7, or vice versa, observed using the FRET peptide substrate with methoxycoumarin (Mca)/dinitrophenyl (Dnp) as fluorophore/quencher, designed and synthesized to obtain the lowest Km value for this substrate, showed approximately a 60% increase in the activity of hMMP2 upon incubation of Bs-Tx7 with the enzyme at a micromolar concentration (4 μM), indicating the importance of this toxin in diseases associated with decreased MMP2 activity.
The Recombinant Bacteriophage Endolysin HY-133 Exhibits In Vitro Activity against Different African Clonal Lineages of the Staphylococcus aureus Complex, Including Staphylococcus schweitzeri
2016-02-02

ABSTRACT HY-133 is a recombinant bacteriophage endolysin with bactericidal activity against Staphylococcus aureus . Here, HY-133 showed in vitro activity against major African methicillin-susceptible and methicillin-resistant S. aureus lineages and ceftaroline/ceftobiprole- and borderline oxacillin-resistant isolates. HY-133 was also active against Staphylococcus schweitzeri , a recently described species of the S. aureus complex. The activity of HY-133 on the tested isolates (MIC 50 , 0.25 μg/ml; MIC 90 , 0.5 μg/ml; range, 0.125 to 0.5 μg/ml) was independent of the species and strain background or antibiotic resistance.
Comparing Hamiltonians of a spinning test particle for different tetrad fields
2016-02-02

This work is concerned with suitable choices of tetrad fields and coordinate\\nsystems for the Hamiltonian formalism of a spinning particle derived in [E.\\nBarausse, E. Racine, and A. Buonanno, Phys. Rev. D 80, 104025 (2009)]. After\\ndemonstrating that with the originally proposed tetrad field the components of\\nthe total angular momentum are not preserved in the Schwarzschild limit, we\\nanalyze other hitherto proposed tetrad choices. Then, we introduce and\\nthoroughly test two new tetrad fields in the horizon penetrating Kerr-Schild\\ncoordinates. Moreover, we show that for the Schwarzschild spacetime background\\nthe linearized in spin Hamiltonian corresponds to an integrable system, while\\nfor the Kerr spacetime we find chaos which suggests a nonintegrable system.\\n
Portals and Web-Based Resources for Virtual Screening
2016-02-02

Virtual screening for active compounds has become an essential step within the drug development pipeline. The computer based prediction of compound binding modes is one of the most time and cost efficient methods for screening ligand libraries and enrich results of potential drugs. Here we present an overview about currently available online resources regarding compound databases, docking applications, and science gateways for drug discovery and virtual screening, in order to help structural biologists in choosing the best tools for their analysis. The appearance of the user interface, authentication and security aspects, data management, and computational performance will be discussed. We anticipate a broad overview about currently available solutions, guiding computational chemists and users from related fields towards scientifically reliable results.
Highly sensitive troponin and coronary computed tomography angiography in the evaluation of suspected acute coronary syndrome in the emergency department
2016-02-02

The evaluation of patients presenting to the emergency department with suspected acute coronary syndrome (ACS) remains a clinical challenge. The traditional assessment includes clinical risk assessment based on cardiovascular risk factors with serial electrocardiograms and cardiac troponin measurements, often followed by advanced cardiac testing as inpatient or outpatient (i.e. stress testing, imaging). Despite this costly and lengthy work-up, there is a non-negligible rate of missed ACS with an increased risk of death. There is a clinical need for diagnostic strategies that will lead to rapid and reliable triage of patients with suspected ACS. We provide an overview of the evidence for the role of highly sensitive troponin (hsTn) in the rapid and efficient evaluation of suspected ACS. Results of recent research studies have led to the introduction of hsTn with rapid rule-in and rule-out protocols into the guidelines. Highly sensitive troponin increases the sensitivity for the detection of myocardial infarction and decreases time to diagnosis; however, it may decrease the specificity, especially when used as a dichotomous variable, rather than continuous variable as recommended by guidelines; this may increase clinician uncertainty. We summarize the evidence for the use of coronary computed tomography angiography (CTA) as the rapid diagnostic tool in this population when used with conventional troponin assays. Coronary CTA significantly decreases time to diagnosis and discharge in patients with suspected ACS, while being safe. However, it may lead to increase in invasive procedures and includes radiation exposure. Finally, we outline the opportunities for the combined use of hsTn and coronary CTA that may result in increased efficiency, decreased need for imaging, lower cost, and decreased radiation dose.
On the Structure of Neuronal Population Activity under Fluctuations in Attentional State
2016-02-03

Attention is commonly thought to improve behavioral performance by increasing response gain and suppressing shared variability in neuronal populations. However, both the focus and the strength of attention are likely to vary from one experimental trial to the next, thereby inducing response variability unknown to the experimenter. Here we study analytically how fluctuations in attentional state affect the structure of population responses in a simple model of spatial and feature attention. In our model, attention acts on the neural response exclusively by modulating each neuron's gain. Neurons are conditionally independent given the stimulus and the attentional gain, and correlated activity arises only from trial-to-trial fluctuations of the attentional state, which are unknown to the experimenter. We find that this simple model can readily explain many aspects of neural response modulation under attention, such as increased response gain, reduced individual and shared variability, increased correlations with firing rates, limited range correlations, and differential correlations. We therefore suggest that attention may act primarily by increasing response gain of individual neurons without affecting their correlation structure. The experimentally observed reduction in correlations may instead result from reduced variability of the attentional gain when a stimulus is attended. Moreover, we show that attentional gain fluctuations, even if unknown to a downstream readout, do not impair the readout accuracy despite inducing limited-range correlations, whereas fluctuations of the attended feature can in principle limit behavioral performance. SIGNIFICANCE STATEMENT Covert attention is one of the most widely studied examples of top-down modulation of neural activity in the visual system. Recent studies argue that attention improves behavioral performance by shaping of the noise distribution to suppress shared variability rather than by increasing response gain. Our work shows, however, that latent, trial-to-trial fluctuations of the focus and strength of attention lead to shared variability that is highly consistent with known experimental observations. Interestingly, fluctuations in the strength of attention do not affect coding performance. As a consequence, the experimentally observed changes in response variability may not be a mechanism of attention, but rather a side effect of attentional allocation strategies in different behavioral contexts.
Metallothioneins and renal ageing
2016-02-03

Increased expression of MTs in the kidney with ageing might be a protective mechanism against increased oxidative stress, which is closely related to the ageing process. Our findings indicate that MTs are functionally involved in the pathophysiology of ageing-related processes.
Benchmark data set for wheat growth models: field experiments and AgMIP multi-model simulations
2016-02-03

The data set includes a current representative management treatment from detailed, quality-tested sentinel field experiments with wheat from four contrasting environments including Australia, The Netherlands, India and Argentina. Measurements include local daily climate data (solar radiation, maximum and minimum temperature, precipitation, surface wind, dew point temperature, relative humidity, and vapor pressure), soil characteristics, frequent growth, nitrogen in crop and soil, crop and soil water and yield components. Simulations include results from 27 wheat models and a sensitivity analysis with 26 models and 30 years (1981-2010) for each location, for elevated atmospheric CO2 and temperature changes, a heat stress sensitivity analysis at anthesis, and a sensitivity analysis with soil and crop management variations and a Global Climate Model end-century scenario. Data access via DOI 10.17026/DANS-ZB6-6FVQ.
A New Method for Re-Analyzing Evaluation Bias: Piecewise Growth Curve Modeling Reveals an Asymmetry in the Evaluation of Pro and Con Arguments
2016-02-03

In four studies we tested a new methodological approach to the investigation of evaluation bias. The usage of piecewise growth curve modeling allowed for investigation into the impact of people's attitudes on their persuasiveness ratings of pro- and con-arguments, measured over the whole range of the arguments' polarity from an extreme con to an extreme pro position. Moreover, this method provided the opportunity to test specific hypotheses about the course of the evaluation bias within certain polarity ranges. We conducted two field studies with users of an existing online information portal (Studies 1a and 2a) as participants, and two Internet laboratory studies with mostly student participants (Studies 1b and 2b). In each of these studies we presented pro- and con-arguments, either for the topic of MOOCs (massive open online courses, Studies 1a and 1b) or for the topic of M-learning (mobile learning, Studies 2a and 2b). Our results indicate that using piecewise growth curve models is more appropriate than simpler approaches. An important finding of our studies was an asymmetry of the evaluation bias toward pro- or con-arguments: the evaluation bias appeared over the whole polarity range of pro-arguments and increased with more and more extreme polarity. This clear-cut result pattern appeared only on the pro-argument side. For the con-arguments, in contrast, the evaluation bias did not feature such a systematic picture.
The emerging role of myeloid-derived suppressor cells in lung diseases
2016-02-04

Myeloid-derived suppressor cells (MDSCs) are innate immune cells characterised by their potential to control T-cell responses and to dampen inflammation. While the role of MDSCs in cancer has been studied in depth, our understanding of their relevance for infectious and inflammatory disease conditions has just begun to evolve. Recent studies highlight an emerging and complex role for MDSCs in pulmonary diseases. In this review, we discuss the potential contribution of MDSCs as biomarkers and therapeutic targets in lung diseases, particularly lung cancer, tuberculosis, chronic obstructive pulmonary disease, asthma and cystic fibrosis.
Discovery of a variable X-ray counterpart to HESS J1832−093: a new gamma-ray binary?
2016-02-04

The TeV gamma-ray point source HESS J1832−093 remains unidentified despite extensive multiwavelength studies. The gamma-ray emission could originate in a very compact pulsar wind nebula or an X-ray binary system composed of the X-ray source XMMU J183245−0921539, and a companion star (2MASS J18324516−0921545). To unveil the nature of XMMU J183245−0921539 and its relation to HESS J1832−093, we performed deeper follow-up observations in X-rays with Chandra and Swift to improve source localization and to investigate time variability. We observed an increase of the X-ray flux by a factor of ∼6 in the Chandra data compared to previous observations. The source is point-like for Chandra and its updated position is only 0.3 arcsec offset from 2MASS J18324516−0921545, confirming the association with this infrared source. Subsequent Swift target of opportunity observations resulted in a lower flux, again compatible with the one previously measured with XMM–Newton, indicating a variability time-scale of the order of two months or shorter. The now-established association of XMMU J183245−0921539 and 2MASS J18324516−0921545, and the observed variability in X-rays are strong evidence for binary nature of HESS J1832−093. Furthermore, observations to characterize the optical counterpart as well as to search for orbital periodicity are needed to confirm this scenario.
Probing Chromatin-modifying Enzymes with Chemical Tools
2016-02-04

Chromatin is the universal template of genetic information in all eukaryotic organisms. Chemical modifications of the DNA-packaging histone proteins and the DNA bases are crucial signaling events in directing the use and readout of eukaryotic genomes. The enzymes that install and remove these chromatin modifications as well as the proteins that bind these marks govern information that goes beyond the sequence of DNA. Therefore, these so-called epigenetic regulators are intensively studied and represent promising drug targets in modern medicine. We summarize and discuss recent advances in the field of chemical biology that have provided chromatin research with sophisticated tools for investigating the composition, activity, and target sites of chromatin modifying enzymes and reader proteins.
Visualizing tropoelastin in a long-term human elastic fibre cell culture model
2016-02-04

Abstract Elastin is an essential protein found in a variety of tissues where resilience and flexibility are needed, such as the skin and the heart. When aiming to engineer suitable implants, elastic fibres are needed to allow adequate tissue renewal. However, the visualization of human elastogenesis remains in the dark. To date, the visualization of human tropoelastin (TE) production in a human cell context and its fibre assembly under live cell conditions has not been achieved. Here, we present a long-term cell culture model of human dermal fibroblasts expressing fluorescence-labelled human TE. We employed a lentiviral system to stably overexpress Citrine-labelled TE to build a fluorescent fibre network. Using immunofluorescence, we confirmed the functionality of the Citrine-tagged TE. Furthermore, we visualized the fibre assembly over the course of several days using confocal microscopy. Applying super resolution microscopy, we were able to investigate the inner structure of the elastin–fibrillin-1 fibre network. Future investigations will allow the tracking of TE produced under various conditions. In tissue engineering applications the fluorescent fibre network can be visualized under various conditions or it serves as a tool for investigating fibre degradation processes in disease-in-a-dish-models.
Fish remains from the Neolithic site of El Mirador cave (Atapuerca, Spain): Seasonality and resource management
2016-02-04

Ichthyoarchaeological analyses of the freshwater fish remains from levels 19 and 20 in El Mirador cave (Atapuerca, Spain) have been conducted. Fish were always present as a source of animal protein, although their importance in the human diet was not fully exploited by people during the Neolithic on the Iberian Peninsula. Two principal goals are treated here: a taxonomic study of the fish remains and a characterization of the exploitation of this resource. The results show that the human community of El Mirador cave practiced fishing, and that fish was part of their diet and social life. Des analyses ichthyo-archéologiques de restes de poissons d'eau douce provenant des niveaux 19 et 20 de la grotte du Mirador (Atapuerda, Espagne) ont été réalisées. Les poissons étaient toujours présents en tant que source de protéine animale, bien que leur importance dans l'alimentation humaine n'ait pas été pleinement explorée au cours du Néolithique dans la péninsule Ibérique. Deux objectifs principaux sont abordés : une étude taxonomique des restes de poisson et une caractérisation de l'exploitation de cette ressource. Les résultats montrent que la communauté humaine de la grotte du Mirador pratiquait la pêche et que le poisson faisait partie de son alimentation et de sa vie sociale.
Inside Back Cover: The Largest Metalloid Group 14 Cluster, Ge18[Si(SiMe3)3]6: An Intermediate on the Way to Elemental Germanium (Angew. Chem. Int. Ed. 9/2016)
2016-02-04

The seemingly simple process of the formation or dissolution of a metal is highly dynamic and mostly unknown on the atomic scale. In their Communication on page 3216 ff., A. Schnepf et al. show that the oxidation of [Ge9(Hyp)3]− (Hyp=Si(SiMe3)3) with an iron(II) salt leads to Ge18(Hyp)6, the largest metalloid Group 14 cluster that has been structurally characterized to date. This cluster can be regarded as a first trapped intermediate of the formation of Ge(cF136) from Ge9 units.
Understanding the detector behavior through Montecarlo and calibration studies in view of the SOX measurement
2016-02-05

Borexino is an unsegmented neutrino detector operating at LNGS in central Italy. The experiment has shown its performances through its unprecedented accomplishments in the solar and geoneutrino detection. These performances make it an ideal tool to accomplish a state- of-the-art experiment able to test the existence of sterile neutrinos (SOX experiment). For both the solar and the SOX analysis, a good understanding of the detector response is fundamental. Consequently, calibration campaigns with radioactive sources have been performed over the years. The calibration data are of extreme importance to develop an accurate Monte Carlo code. This code is used in all the neutrino analyses. The Borexino-SOX calibration techniques and program and the advances on the detector simulation code in view of the start of the SOX data taking are presented. 1
Continuum correlations in accreting X-ray pulsars
2016-02-05

Two-dimensional structure of accretion columns in the radiation-diffusion limit is calculated for two possible geometries (filled and hollow cylinder) for mass accretion rates ranging from 1017 to 1.2 x 1018 g s-1. The observed spectral hardening in the transient X-ray pulsars with increasing can be reproduced by a Compton-saturated sidewall emission from optically thick magnetized accretion columns with taking into account the emission reflected from the neutron star atmosphere. At above some critical value cr ∼ (6 — 8) x 1017 g s-1, the height of the column becomes such that the contribution of the reflected component to the total emission starts decreasing, which leads to the saturation and even slight decrease of the spectral hardness. Hollow-cylinder columns have a smaller height than the filled-cylinder ones, and the contribution of the reflected component in the total emission does not virtually change with (and hence the hardness of the continuum monotonically increases) up to higher mass accretion rates than cr for the filled columns.
The high precision measurement of the144Ce activity in the SOX experiment
2016-02-05

In order to perform a resolutive measurement to clarify the neutrino anomalies and to observe possible short distance neutrino oscillations, the SOX (Short distance neutrino Oscillations with BoreXino) experiment is under construction. In the first phase, a 100 kCi 144Ce-144Pr antineutrino source will be placed under the Borexino detector at the Laboratori Nazionali del Gran Sasso (LNGS), in center of Italy, and the rate measurement of the antineutrino events, observed by the very low radioactive background Borexino detector, will be compared with the high precision (&amp;lt; 1%) activity measurement performed by two calorimeters. The source will be embedded in a 19 mm thick tungsten alloy shield and both the calorimeters have been conceived for measuring the thermal heat absorbed by a water flow. In this report the design of the calorimeters will be described in detail and very preliminary results will be also shown.
Whose “Storm and Stress” Is It? Parent and Child Reports of Personality Development in the Transition to Early Adolescence
2016-02-06

Abstract The present study investigated Big Five personality trait development in the transition to early adolescence (from the fifth to eighth grade). Personality traits were assessed in 2,761 (47% female) students over a 3‐year period of time. Youths’ self‐reports and parent ratings were used to test for cross‐informant agreement. Acquiescent responding and measurement invariance were established with latent variable modeling. Growth curve models revealed three main findings: (a) Normative mean‐level changes occurred for youths’ self‐report data and parent ratings with modest effects in both cases. (b) Agreeableness and Openness decreased for self‐reports and parent ratings, whereas data source differences were found for Conscientiousness (decreased for self‐reports and remained stable for parent ratings), Extraversion (increased for self‐reports and decreased for parent ratings), and Neuroticism (remained stable for self‐reports and decreased for parent ratings). (c) Girls showed a more mature personality overall (self‐reports and parent ratings revealed higher levels of Agreeableness, Conscientiousness, and Openness) and became more extraverted in the middle of adolescence (self‐reports). Personality changes modestly during early adolescence whereby change does not occur in the direction of maturation, and substantial differences exist between parent ratings and self‐reports.
Neutrophils in cystic fibrosis
2016-02-06

Abstract Cystic fibrosis (CF) lung disease is characterized by chronic infection and inflammation. Among inflammatory cells, neutrophils represent the major cell population accumulating in the airways of CF patients. While neutrophils provide the first defensive cellular shield against bacterial and fungal pathogens, in chronic disease conditions such as CF these short-lived immune cells release their toxic granule contents that cause tissue remodeling and irreversible structural damage to the host. A variety of human and murine studies have analyzed neutrophils and their products in the context of CF, yet their precise functional role and therapeutic potential remain controversial and incompletely understood. Here, we summarize the current evidence in this field to shed light on the complex and multi-faceted role of neutrophils in CF lung disease.