julilili42/papers huggingface dataset:
Ursolic acid and carvacrol may be potential inhibitors of dormancy protein small heat shock protein16.3 of Mycobacterium tuberculosis
2017-10-06

Small heat shock protein16.3 (sHSP16.3) is a crucial protein for survival of Mycobacterium tuberculosis (MTB) in its host. Besides, this protein acts as a molecular chaperone during stress and is indispensable for MTB's growth, virulence and cell-wall thickening. sHSP16.3 is also a promising candidate for vaccine, serodiagnosis and drug design as well. In the present study, we have targeted sHSP16.3 with two phytochemicals, namely ursolic acid and carvacrol using in silico approach. Molecular docking analysis showed that both phytochemicals (ursolic acid and carvacrol) have docked with sHSP16.3 and shown tendency to inhibit the function of this vital protein of MTB. In addition, both compounds have exhibited strong compatibility with sHSP16.3 during whole 60 ns duration of molecular dynamics simulation. Further, the molecular mechanic/generalized Born/Poisson-Boltzmann surface area (MM/G/P/BSA) free energies were calculated which showed that both phytocompounds have stable and favourable binding energies causing strong binding with binding site of sHSP16.3. Taking together, the data of present study suggest that both phytocompounds may be potential inhibitor of sHSP16.3 of MTB and a best alternative to standard anti-tuberculosis drugs.
Luminescence Quenching of Ligand‐Substituted Molybdenum and Tungsten Halide Clusters by Oxygen and Their Oxidation Electrochemistry
2017-10-06

Cluster compounds (TBA) 2 [Mo 6 I 8 (CF 3 SO 3 ) 6 ], (TBA) 2 [W 6 I 8 (CF 3 SO 3 ) 6 ], and (TBA) 2 [W 6 Br 8 (CF 3 SO 3 ) 6 ] are prepared and structurally characterized from single‐crystal X‐ray diffraction data. All compounds show red emission on photoexcitation at 400 nm. However, the phosphorescence of crystalline samples is quenched in the presence of oxygen, depending on the partial pressure of oxygen. The distinct phosphorescence‐quenching behavior of compounds containing trifluoromethanesulfonato (CF 3 SO 3 – ) ligands is compared with corresponding compounds with trifluoroacetato (CF 3 COO – ) and p ‐toluolsulfonato (CH 3 C 6 H 4 SO 3 – ) ligands. By studying these compounds, we investigate the relationship of more‐ or less‐electron‐withdrawing ligands (L) of (TBA) 2 [M 6 X 8 L 6 ] halide (X) clusters, their redox potentials ( E 0 ), and their phosphorescence‐quenching behavior under variable oxygen partial pressures.
Who depends on whom? On the relation between Peter Lombard’s commentary on Romans and the one of Herveus of Bourg-Dieu
2017-10-06

In this article, Peter Lombard’s commentary on Romans is compared with the one of Herveus of Bourg-Dieu by questioning, if there is a dependency between both. The comparison shows, that either there was an unknown common source which was used by both of them, or Peter Lombard used the Enarrationes of Herveus of Bourg-Dieu; the second hypothesis is more probable and argues for dating the Lombard’s Collectanea on 1148 or later.
The bulky and the sweet: How neutralizing antibodies and glycan receptors compete for virus binding
2017-10-07

Abstract Numerous viruses rely on glycan receptor binding as the initial step in host cell infection. Engagement of specific glycan receptors such as sialylated carbohydrates, glycosaminoglycans, or histo‐blood group antigens can determine host range, tissue tropism, and pathogenicity. Glycan receptor‐binding sites are typically located in exposed regions on viral surfaces—sites that are also generally prone to binding of neutralizing antibodies that directly interfere with virus‐glycan receptor interactions. In this review, we examine the locations and architecture of the glycan‐ and antibody‐binding sites in four different viruses with stalk‐like attachment proteins (reovirus, influenza virus, norovirus, and coronavirus) and investigate the mechanisms by which antibodies block glycan recognition. Those viruses exemplify that direct molecular mimicking of glycan receptors by antibodies is rare and further demonstrate that antibodies often partly overlap or bind sufficiently close to the receptor‐binding region to hinder access to this site, achieving neutralization partially because of the epitope location and partly due to their sheer size.
Symmetric multistep methods for charged-particle dynamics
2017-10-08

A class of explicit symmetric multistep methods is proposed for integrating the equations of motion of charged particles in an electro-magnetic field. The magnetic forces are built into these methods in a special way that respects the Lagrangian structure of the problem. It is shown that such methods approximately preserve energy and momentum over very long times, proportional to a high power of the inverse stepsize. We explain this behaviour by studying the modified differential equation of the methods and by analysing the remarkably stable propagation of parasitic solution components.
Impact of Social Cognition on Alcohol Dependence Treatment Outcome: Poorer Facial Emotion Recognition Predicts Relapse/Dropout
2017-10-09

Background Despite growing evidence for neurobehavioral deficits in social cognition in alcohol use disorder (AUD), the clinical relevance remains unclear, and little is known about its impact on treatment outcome. This study prospectively investigated the impact of neurocognitive social abilities at treatment onset on treatment completion. Methods Fifty‐nine alcohol‐dependent patients were assessed with measures of social cognition including 3 core components of empathy via paradigms measuring: (i) emotion recognition (the ability to recognize emotions via facial expression), (ii) emotional perspective taking, and (iii) affective responsiveness at the beginning of inpatient treatment for alcohol dependence. Subjective measures were also obtained, including estimates of task performance and a self‐report measure of empathic abilities (Interpersonal Reactivity Index). According to treatment outcomes, patients were divided into a patient group with a regular treatment course (e.g., with planned discharge and without relapse during treatment) or an irregular treatment course (e.g., relapse and/or premature and unplanned termination of treatment, “dropout”). Results Compared with patients completing treatment in a regular fashion, patients with relapse and/or dropout of treatment had significantly poorer facial emotion recognition ability at treatment onset. Additional logistic regression analyses confirmed these results and identified poor emotion recognition performance as a significant predictor for relapse/dropout. Self‐report (subjective) measures did not correspond with neurobehavioral social cognition measures, respectively objective task performance. Analyses of individual subtypes of facial emotions revealed poorer recognition particularly of disgust, anger, and no (neutral faces) emotion in patients with relapse/dropout. Conclusions Social cognition in AUD is clinically relevant. Less successful treatment outcome was associated with poorer facial emotion recognition ability at the beginning of treatment. Impaired facial emotion recognition represents a neurocognitive risk factor that should be taken into account in alcohol dependence treatment. Treatments targeting the improvement of these social cognition deficits in AUD may offer a promising future approach.
The Cysteinome of Protein Kinases as a Target in Drug Development
2017-10-10

Abstract Drugs that function through covalent bond formation represent a considerable fraction of our repository of effective medicines but safety concerns and the complexity of developing covalent inhibitors has rendered covalent targeting a less attractive strategy for rational drug design. The recent approval of four covalent kinase inhibitors and the development of highly potent covalent kinase probes with exceptional selectivity has raised significant interest in industry and academic research and validated the concept of covalent kinase targeting for clinical applications. The abundance of cysteines at diverse positions in and around the kinase active site suggests that a large fraction of kinases can be targeted by covalent inhibitors. Herein, we review recent developments of this rapidly growing area in kinase drug development and highlight the unique opportunities and challenges of this strategy.
Photoreactions of Phenylborylene with Dinitrogen and Carbon Monoxide
2017-10-10

Formal removal of two bonding partners from boranes, BR<sub>3</sub>, yields borylenes, RB, which have been inferred as reactive intermediates in a number of reactions. Phenylborylene (R = C<sub>6</sub>H<sub>5</sub>; 1) is accessible from phenyldiazidoborane by photochemical extrusion of dinitrogen under matrix isolation conditions. Concomitantly, the nitrene PhNBN is formed via phenyl rearrangement. Here we used a combination of UV/vis, IR, and ESR spectroscopy under cryogenic matrix isolation conditions to investigate the properties and reactivity of phenylborylene. We detected an absorption band of phenylborylene at 375 nm (S<sub>0</sub> → S<sub>2</sub>) and tentatively assigned the S<sub>0</sub> → S<sub>1</sub> transition to a very weak band at 518 nm. We also show for the first time that an electrophilic borylene such as 1 can react with N<sub>2</sub> reversibly and with CO irreversibly under photochemical conditions. The corresponding photoproducts PhBNN and PhBCO have triplet electronic ground states. Their small E values are in agreement with the linear arrangements Ph-B-N-N and Ph-B-C-O obtained by density functional theory computations. The D values decrease in the series PhNBN > PhBNN > PhBCO and approach the value for phenylcarbene (PhCH). Indeed, the boron center in PhBCO is isoelectronic with the carbene center in PhCH. The compounds are the first examples of boron analogues of diazoalkanes (R<sub>2</sub>CNN) and ketenes (R<sub>2</sub>CCO), and their formation may serve as a demonstration of the high reactivity of phenylborylene.
mRNA transport in fungal top models
2017-10-10

Eukaryotic cells rely on the precise determination of when and where proteins are synthesized. Spatiotemporal expression is supported by localization of mRNAs to specific subcellular sites and their subsequent local translation. This holds true for somatic cells as well as for oocytes and embryos. Most commonly, mRNA localization is achieved by active transport of the molecules along the actin or microtubule cytoskeleton. Key factors are molecular motors, adaptors, and RNA‐binding proteins that recognize defined sequences or structures in cargo mRNAs. A deep understanding of this process has been gained from research on fungal model systems such as Saccharomyces cerevisiae and Ustilago maydis . Recent highlights of these studies are the following: (1) synergistic binding of two RNA‐binding proteins is needed for high affinity recognition; (2) RNA sequences undergo profound structural rearrangements upon recognition; (3) mRNA transport is tightly linked to membrane trafficking; (4) mRNAs and ribosomes are transported on the cytoplasmic surface of endosomes; and (5) heteromeric protein complexes are, most likely, assembled co‐translationally during endosomal transport. Thus, the study of simple fungal model organisms provides valuable insights into fundamental mechanisms of mRNA transport boosting the understanding of similar events in higher eukaryotes. WIREs RNA 2018, 9:e1453. doi: 10.1002/wrna.1453 This article is categorized under: RNA Interactions with Proteins and Other Molecules &gt; Protein–RNA Recognition RNA Interactions with Proteins and Other Molecules &gt; RNA–Protein Complexes RNA Export and Localization &gt; RNA Localization
An Accurate Model for the Ion Current–Distance Behavior in Scanning Ion Conductance Microscopy Allows for Calibration of Pipet Tip Geometry and Tip–Sample Distance
2017-10-10

The scanning ion conductance microscope (SICM) is an emerging tool for noncontact topography imaging and multiphysical investigation of soft samples in aqueous environments such as living cells. Despite the increasing popularity of SICM, several aspects of the imaging process are still unknown; for example, there is still no accurate description of the behavior of the ion current for a varying tip-sample distance. To predict this ion current-distance behavior, we provide a new numerical model based on finite element modeling. The model allows, for the first time, accurately determining the tip-sample distance during an SICM experiment. Furthermore, we present a nondestructive method for calibrating the pipet tip geometry by fitting the numerical model to the experimental ion current-distance data and verify this method using pipets with opening radii between 30 and 300 nm.
Patient acceptable symptom state in scleroderma: results from the tocilizumab compared with placebo trial in active diffuse cutaneous systemic sclerosis
2017-10-10

PASS may be used as a patient-centred outcome in SSc, especially as a 7-point Likert scale. Further validation is required to determine the utility as an outcome measure in trials and clinical practice.
The 100 most influential papers about cataract surgery: a bibliometric analysis
2017-10-10

To our knowledge, this is the first study on the most influential papers in cataract surgery after a comprehensive research of relevant literatures. The present work may provide us concise information concerning the development history of cataract surgery over the past 66y.
THE WATER MITES OF THE GENUS HYDRODROMA (ACARI, HYDRACHNIDIA, HYDRODROMIDAE) IN EUROPE AND AFRICA
2017-10-10

Neotypes are designated for Hydrodroma despiciens (Müller, 1776) and H. pilosa Besseling, 1940, lectotypes for H. torrenticola (Walter, 1908) and H. capensis (K. Viets, 1914). Diagnostic features and morphological variability of these two species, as well as of H. torrenticola and H. perreptans, are discussed. New morphological details are presented for H. trigonometrica Walter, 1928, H. ocellata Walter &amp; Bader, 1952 (here considered a species incerta), H. liberiensis Cook, 1966 and H. reinhardi Pešić, 2002. After revision of museum collections, numerous older identifications are corrected. Concerning material from Europe, a high degree of confusion is found between H. despiciens, H. torrenticola and H. pilosa. For H. despiciens, all records from Africa, as well as species identifications from Wisconsin (U.S.A) and Argentina are rejected. This species, formerly considered cosmopolitan, is actually ascertained only from the European continent. Hydrodroma pilosa is recorded for the first time from Africa (Algeria). Most published records of H. capensis refer to other, in several cases probably undescribed species; recognized material derives exclusively from the terra typica in the African Cape Province. An identification key is given for the species known from Europe and Africa.
Interacting Learning Processes during Skill Acquisition: Learning to control with gradually changing system dynamics
2017-10-10

Abstract There is increasing evidence that sensorimotor learning under real-life conditions relies on a composition of several learning processes. Nevertheless, most studies examine learning behaviour in relation to one specific learning mechanism. In this study, we examined the interaction between reward-based skill acquisition and motor adaptation to changes of object dynamics. Thirty healthy subjects, split into two groups, acquired the skill of balancing a pole on a cart in virtual reality. In one group, we gradually increased the gravity, making the task easier in the beginning and more difficult towards the end. In the second group, subjects had to acquire the skill on the maximum, most difficult gravity level. We hypothesized that the gradual increase in gravity during skill acquisition supports learning despite the necessary adjustments to changes in cart-pole dynamics. We found that the gradual group benefits from the slow increment, although overall improvement was interrupted by the changes in gravity and resulting system dynamics, which caused short-term degradations in performance and timing of actions. In conclusion, our results deliver evidence for an interaction of reward-based skill acquisition and motor adaptation processes, which indicates the importance of both processes for the development of optimized skill acquisition schedules.
Deep convolutional models improve predictions of macaque V1 responses to natural images
2017-10-11

Abstract Despite great efforts over several decades, our best models of primary visual cortex (V1) still predict spiking activity quite poorly when probed with natural stimuli, highlighting our limited understanding of the nonlinear computations in V1. Recently, two approaches based on deep learning have been successfully applied to neural data: On the one hand, transfer learning from networks trained on object recognition worked remarkably well for predicting neural responses in higher areas of the primate ventral stream, but has not yet been used to model spiking activity in early stages such as V1. On the other hand, data-driven models have been used to predict neural responses in the early visual system (retina and V1) of mice, but not primates. Here, we test the ability of both approaches to predict spiking activity in response to natural images in V1 of awake monkeys. Even though V1 is rather at an early to intermediate stage of the visual system, we found that the transfer learning approach performed similarly well to the data-driven approach and both outperformed classical linear-nonlinear and wavelet-based feature representations that build on existing theories of V1. Notably, transfer learning using a pre-trained feature space required substantially less experimental time to achieve the same performance. In conclusion, multi-layer convolutional neural networks (CNNs) set the new state of the art for predicting neural responses to natural images in primate V1 and deep features learned for object recognition are better explanations for V1 computation than all previous filter bank theories. This finding strengthens the necessity of V1 models that are multiple nonlinearities away from the image domain and it supports the idea of explaining early visual cortex based on high-level functional goals. Author summary Predicting the responses of sensory neurons to arbitrary natural stimuli is of major importance for understanding their function. Arguably the most studied cortical area is primary visual cortex (V1), where many models have been developed to explain its function. However, the most successful models built on neurophysiologists’ intuitions still fail to account for spiking responses to natural images. Here, we model spiking activity in primary visual cortex (V1) of monkeys using deep convolutional neural networks (CNNs), which have been successful in computer vision. We both trained CNNs directly to fit the data, and used CNNs trained to solve a high-level task (object categorization). With these approaches, we are able to outperform previous models and improve the state of the art in predicting the responses of early visual neurons to natural images. Our results have two important implications. First, since V1 is the result of several nonlinear stages, it should be modeled as such. Second, functional models of entire visual pathways, of which V1 is an early stage, do not only account for higher areas of such pathways, but also provide useful representations for V1 predictions.
Production of drop-in fuels from biomass at high selectivity by combined microbial and electrochemical conversion
2017-10-11

Renewable electrical energy production, such as wind power or photovoltaics, faces temporal fluctuations and spatial separation of source and sink creating the need for suitable storage and conversion technologies. Furthermore, a bio-based economy needs technologies allowing the on-demand and on-site conversion of biomass to platform chemicals and chemical energy carriers. This study combines microbial and electrochemical conversions, allowing production of chemicals from biomass and electricity. Carboxylic acids (CAs) are produced by anaerobic conversion of a renewable feedstock with reactor microbiomes. CAs are subsequently electrochemically upgraded to yield energy-dense alkanes. We present a proof-of-concept based on experimental data for each step in two independent case studies at laboratory scale. During continuous CA fermentation from corn beer, mainly n-caproic and n-caprylic acid were produced yielding in total 0.638 g COD g−1 COD [CA/corn beer]. A batch system fed with corn silage yielded mainly n-butyric acid (0.207 g COD g−1 COD [CA/corn silage]), and some n-caproic acid (0.030 g COD g−1 COD [CA/corn silage]). The CAs were removed from the fermentation broth using a pertraction system. Subsequently, the CAs were electrochemically converted via Kolbe reaction and other reaction pathways. Depending on the carbon chain length of the CAs, liquid alkanes (from medium-chain CAs) or gaseous alkanes and alcohols (from short-chain CAs) were gained. Coulombic efficiencies of up to 80% were achieved despite the alkaline (pH 9) electrolysis conditions that are dictated by the pertraction system. Remarkably, CAs with a carbon chain length of six or more C-atoms were successfully converted to liquid alkanes at a high yield (in total: 0.480 g COD g−1 COD [hydrocarbon/corn beer]). This was achieved at an energy input of only 0.100 kW h per mol of converted CA (considering the electrochemical half cell reaction). Noteworthily, the electrochemical CA conversion is much faster than the CA fermentation, allowing intermittent electrolysis during periods of excess electrical power. We demonstrate that the finally gained product is suitable as a drop-in fuel without any further downstream processing. The future general potential as well as requirements for the concept are discussed.
Fluorenyl Half-Sandwich Bis(tetramethylaluminate) Complexes of the Rare-Earth Metals: Synthesis, Structure, and Isoprene Polymerization
2017-10-11

Aiming at half-sandwich complexes of the type (FluR)Ln(AlMe4)2, homoleptic tetramethylaluminates Ln(AlMe4)3 (Ln = Y, La, Nd, and Lu) were treated with equimolar amounts of R-substituted potassium fluorenyls. The salt metathesis reaction of La(AlMe4)3 with K(Flu) (Flu = fluorenyl = C13H9) and K(FlutBu) (FlutBu = di(tert-butyl) fluorenyl) selectively gave the desired half-sandwich complexes (FluR)La(AlMe4)2. The corresponding reactions of Y(AlMe4)3 with K(Flu)/K(FlutBu) and Lu(AlMe4)3 with K(FlutBu) gave mixtures of half-sandwich and sandwich complexes, while treatment of Lu(AlMe4)3 with K(Flu) produced only the lutetocene complex (Flu)2Lu(AlMe4). Sterically more demanding 1-trimethylsilyl fluorenyl (FluSi) allowed for the isolation of half-sandwich complexes for the entire Ln(III) size range (Ln = La, Nd, Y, and Lu), in crystalline yields up to 94%. Upon activation with routinely employed borate or borane activators [Ph3C][B(C6F5)4], [PhNMe2H][B(C6F5)4], and B(C6F5)3, highly active initiators for isoprene polymerization were obtained. The catalyst activity as well as molecular weight (distribution) and stereoregularity of the obtained polyisoprenes are governed by the rare-earth metal size, fluorenyl ligand, and cocatalyst: highest activity for La/FluSi/[Ph3C][B(C6F5)4], lowest Mw/Mn = 1.11 for La/Flu/[PhNMe2H][B(C6F5)4], maximum trans-1,4 selectivity = 85% for La/FlutBu/[PhNMe2H][B(C6F5)4], maximum cis-1,4 selectivity = 78% for Lu/FluSi/[Ph3C][B(C6F5)4]. The formations of the active species were investigated by NMR spectroscopy revealing not only established cationization pathways but also fluorenyl abstraction in lanthanum complexes (Flu)La(AlMe4)2 and (FlutBu)La(AlMe4)2 by trityl borate [Ph3C][B(C6F5)4]. The reaction of half-sandwich complexes (FluR)Ln(AlMe4)2 with equimolar amounts of Me2AlCl did not give access to catalytically active species. Crystallization of binary mixtures (FluSi)Y(AlMe4)2/Me2AlCl in distinct molar ratios of 1:1 and 1:1.7 yielded complexes [(FluSi)Y(AlMe4)(μ-Cl)]2 and (FluSi)6Y6Cl12, respectively.