julilili42/papers huggingface dataset:
Membrane Disintegration Caused by the Steroid Saponin Digitonin Is Related to the Presence of Cholesterol
2015-11-09

In the present investigation we studied the molecular mechanisms of the monodesmosidic saponin digitonin on natural and artificial membranes. We measured the hemolytic activity of digitonin on red blood cells (RBCs). Also different lipid membrane models (large unilamellar vesicles, LUVs, and giant unilamellar vesicles, GUVs) in the presence and absence of cholesterol were employed. The stability and permeability of the different vesicle systems were studied by using calcein release assay, GUVs membrane permeability assay using confocal microscopy (CM) and fluorescence correlation spectroscopy (FCS) and vesicle size measurement by dynamic light scattering (DLS). The results support the essential role of cholesterol in explaining how digitonin can disintegrate biological and artificial membranes. Digitonin induces membrane permeability or causes membrane rupturing only in the presence of cholesterol in an all-or-none mechanism. This effect depends on the concentrations of both digitonin and cholesterol. At low concentrations, digitonin induces membrane permeability while keeping the membrane intact. When digitonin is combined with other drugs, a synergistic potentiation can be observed because it facilitates their uptake.
Derivation of Pluripotent Cells from Mouse SSCs Seems to Be Age Dependent
2015-11-09

Here, we aimed to answer important and fundamental questions in germ cell biology with special focus on the age of the male donor cells and the possibility to generate embryonic stem cell‐ (ESC‐) like cells. While it is believed that spermatogonial stem cells (SSCs) and truly pluripotent ESC‐like cells can be isolated from adult mice, it remained unknown if the spontaneous conversion of SSCs to ESC‐like cells fails at some age. Similarly, there have been differences in the literature about the duration of cultures during which ESC‐like cells may appear. We demonstrate the possibility to derive ESC‐like cells from SSC cultures until they reach adolescence or up to 7 weeks of age, but we point out the impossibility to derive these cells from older, mature adult mice. The inability of real adult SSCs to shift to a pluripotent state coincides with a decline in expression of the core pluripotency genes Oct4, Nanog, and Sox2 in SSCs with age. At the same time genes of the spermatogonial differentiation pathway increase. The generated ESC‐like cells were similar to ESCs and express pluripotency markers. In vitro they differentiate into all three germ lineages; they form complex teratomas after transplantation in SCID mice and produce chimeric mice.
Testing and Validation of Computational Methods for Mass Spectrometry
2015-11-09

High-throughput methods based on mass spectrometry (proteomics, metabolomics, lipidomics, etc.) produce a wealth of data that cannot be analyzed without computational methods. The impact of the choice of method on the overall result of a biological study is often underappreciated, but different methods can result in very different biological findings. It is thus essential to evaluate and compare the correctness and relative performance of computational methods. The volume of the data as well as the complexity of the algorithms render unbiased comparisons challenging. This paper discusses some problems and challenges in testing and validation of computational methods. We discuss the different types of data (simulated and experimental validation data) as well as different metrics to compare methods. We also introduce a new public repository for mass spectrometric reference data sets ( http://compms.org/RefData ) that contains a collection of publicly available data sets for performance evaluation for a wide range of different methods.
Multiple Independent Oscillatory Networks in the Degenerating Retina
2015-11-09

During neuronal degenerative diseases, microcircuits undergo severe structural alterations, leading to remodeling of synaptic connectivity. This can be particularly well observed in the retina, where photoreceptor degeneration triggers rewiring of connections in the retina's first synaptic layer (e.g., Strettoi et al., 2003; Haq et al., 2014), while the synaptic organization of inner retinal circuits appears to be little affected (O'Brien et al., 2014; Figures 1A,B). Remodeling of (outer) retinal circuits and diminishing light-driven activity due to the loss of functional photoreceptors lead to spontaneous activity that can be observed at different retinal levels (Figure 1C), including the retinal ganglion cells, which display rhythmic spiking activity in the degenerative retina (Margolis et al., 2008; Stasheff, 2008; Menzler and Zeck, 2011; Stasheff et al., 2011). Two networks have been suggested to drive the oscillatory activity in the degenerating retina: a network of remnant cone photoreceptors, rod bipolar cells (RBCs) and horizontal cells in the outer retina (Haq et al., 2014), and the AII amacrine cell-cone bipolar cell network in the inner retina (Borowska et al., 2011). Notably, spontaneous rhythmic activity in the inner retinal network can be triggered in the absence of synaptic remodeling in the outer retina, for example, in the healthy retina after photo-bleaching (Menzler et al., 2014). In addition, the two networks show remarkable differences in their dominant oscillation frequency range as well as in the types and numbers of involved cells (Menzler and Zeck, 2011; Haq et al., 2014). Taken together this suggests that the two networks are self-sustained and can be active independently from each other. However, it is not known if and how they modulate each other. In this mini review, we will discuss: (i) commonalities and differences between these two oscillatory networks as well as possible interaction pathways; (ii) how multiple self-sustained networks may hamper visual restoration strategies employing, for example, microelectronic implants, optogenetics or stem cells, and briefly; and (iii) how the finding of diverse (independent) networks in the degenerative retina may relate to other parts of the neurodegenerative central nervous system.
Interface control by homoepitaxial growth in pulsed laser deposited iron chalcogenide thin films
2015-11-09

Abstract Thin film growth of iron chalcogenides by pulsed laser deposition (PLD) is still a delicate issue in terms of simultaneous control of stoichiometry, texture, substrate/film interface properties and superconducting properties. The high volatility of the constituents sharply limits optimal deposition temperatures to a narrow window and mainly challenges reproducibility for vacuum based methods. In this work we demonstrate the beneficial introduction of a semiconducting FeSe 1− x Te x seed layer for subsequent homoepitaxial growth of superconducting FeSe 1− x Te x thin film on MgO substrates. MgO is one of the most favorable substrates used in superconducting thin film applications, but the controlled growth of iron chalcogenide thin films on MgO has not yet been optimized and is the least understood. The large mismatch between the lattice constants of MgO and FeSe 1− x Te x of about 11% results in thin films with a mixed texture, that prevents further accurate investigations of a correlation between structural and electrical properties of FeSe 1− x Te x . Here we present an effective way to significantly improve epitaxial growth of superconducting FeSe 1− x Te x thin films with reproducible high critical temperatures (≥17 K) at reduced deposition temperatures (200 °C–320 °C) on MgO using PLD. This offers a broad scope of various applications.
High-velocity gas toward the LMC resides in the Milky Way halo
2015-11-09

To explore the origin of high-velocity gas in the direction of the Large\\nMagellanic Cloud (LMC) we analyze absorption lines in the ultraviolet spectrum\\nof a Galactic halo star that is located in front of the LMC at d=9.2 kpc\\ndistance. We study the velocity-component structure of low and intermediate\\nmetal ions in the spectrum of RXJ0439.8-6809, as obtained with the Cosmic\\nOrigins Spectrograph (COS) onboard HST, and measure equivalent widths and\\ncolumn densities for these ions. We supplement our COS data with a\\nFar-Ultraviolet Spectroscopic Explorer spectrum of the nearby LMC star Sk-69 59\\nand with HI 21cm data from the Leiden-Argentina-Bonn (LAB) survey. Metal\\nabsorption towards RXJ0439.8-6809 is unambiguously detected in three different\\nvelocity components near v_LSR=0,+60, and +150 km/s. The presence of absorption\\nproves that all three gas components are situated in front of the star, thus\\nbeing located in the disk and inner halo of the Milky Way. For the\\nhigh-velocity cloud (HVC) at v_LSR=+150 km/s we derive an oxygen abundance of\\n[O/H]=-0.63 (~0.2 solar) from the neighbouring Sk-69 59 sightline, in\\naccordance with previous abundance measurements for this HVC. From the observed\\nkinematics we infer that the HVC hardly participates in the Galactic rotation.\\nOur study shows that the HVC towards the LMC represents a Milky Way halo cloud\\nthat traces low-column density gas with relatively low metallicity. It rules\\nout scenarios in which the HVC represents material close to the LMC that stems\\nfrom a LMC outflow.\\n
Multifrequency perturbations in matter-wave interferometry
2015-11-09

High contrast matter-wave interferometry is essential in various fundamental\\nquantum mechanical experiments as well as for technical applications. Thereby,\\ncontrast and sensitivity are typically reduced by decoherence and dephasing\\neffects. While decoherence accounts for a general loss of quantum information\\nin a system due to entanglement with the environment, dephasing is due to\\ncollective time-dependent external phase shifts, which can be related to\\ntemperature drifts, mechanical vibrations or electromagnetic oscillations. In\\ncontrast to decoherence, dephasing can in principle be reversed. Here, we\\ndemonstrate in experiment and theory a method for the analysis and reduction of\\nthe influence of dephasing noise and perturbations consisting of several\\nexternal frequencies in an electron interferometer. This technique uses the\\nhigh spatial and temporal resolution of a delay line detector to reveal and\\nremove dephasing perturbations by second order correlation analysis. It allows\\nmatter-wave experiments under perturbingly lab conditions and can be applied in\\nprinciple to electron, atom, ion, neutron and molecule interferometers.\\n
GBA‐associated parkinsonism and dementia: beyond α‐synucleinopathies?
2015-11-09

Abstract Background and purpose To date the role of GBA mutations beyond α‐synucleinopathies in the parkinsonism−dementia spectrum is still unclear. The aim of the study was to screen for GBA mutations in progressive supranuclear palsy ( PSP ), corticobasal syndrome ( CBS ), primary progressive aphasia ( PPA ) and the behavioural variant of frontotemporal dementia (bv FTD ). Methods In all, 303 patients with a clinical diagnosis of PSP ( n = 157), CBS ( n = 39), PPA ( n = 35) and bv FTD ( n = 72) and 587 neurologically healthy controls were screened for the most common GBA mutations. Results GBA mutations were detected in one healthy control and four patients with a clinical diagnosis of PSP ( n = 1), probable CBS ( n = 2) and PPA ( n = 1, with concomitant C9orf72 expansion). Overall the prevalence of GBA mutations was low in non‐α‐synucleinopathies but significantly higher in the CBS subgroup compared to controls. Conclusion Although numbers are small, our findings indicate that the clinical phenotype of GBA ‐associated neurodegenerative disease is more heterogeneous than previously assumed, including phenotypes not usually associated with underlying α‐synucleinopathies. This may be of relevance, once causal therapeutic strategies for GBA ‐associated neurodegenerative disease are developed.
A sinemydid turtle from the Jehol Biota provides insights into the basal divergence of crown turtles
2015-11-10

Abstract Morphological phylogenies stand in a major conflict with molecular hypotheses regarding the phylogeny of Cryptodira, the most diverse and widely distributed clade of extant turtles. However, molecular hypotheses are often considered a better estimate of phylogeny given that it is more consistent with the stratigraphic and geographic distribution of extinct taxa. That morphology fails to reproduce the molecular topology partly originates from problematic character polarization due to yet another contradiction around the composition of the cryptodiran stem lineage. Extinct sinemydids are one of these problematic clades: they have been either placed among stem-cryptodires, stem-chelonioid sea turtles, or even stem-turtles. A new sinemydid from the Early Cretaceous Jehol Biota (Yixian Formation, Barremian-Early Aptian) of China, Xiaochelys ningchengensis gen. et sp. nov., allows for a reassessment of the phylogenetic position of Sinemydidae. Our analysis indicates that sinemydids mostly share symplesiomorphies with sea turtles and their purported placement outside the crown-group of turtles is an artefact of previous datasets. The best current phylogenetic estimate is therefore that sinemydids are part of the stem lineage of Cryptodira together with an array of other Jurassic to Cretaceous taxa. Our study further emphasises the importance of using molecular scaffolds in global turtle analyses.
Hunting Without a Web: How Lycosoid Spiders Subdue their Prey
2015-11-10

Abstract More than half of all spider species hunt prey without a web. To successfully subdue their prey, they use adapted capture behaviour and efficient grasping mechanisms to interrupt the prey's locomotion, and to restrain it from escaping during the subsequent handling for final envenomation. In this study, we investigated how the prey capture behaviour of different lycosoid spider species is related to leg morphology and venom efficiency; using high speed videography, feeding experiments, stereomicroscopy, scanning electron microscopy and LD 50 venom bioassays. We found that different species employed different techniques when grasping their prey and these differences strongly correlate with the distribution and size of hairy adhesive leg pads (so‐called scopulae on pro‐ and retrolateral parts of legs) and erectable spines, which act in a complementary way. Our results indicate that the grasping and handling behaviour and leg morphology is crucial in restricting the prey's movements. However, none of these traits is directly related with venom efficiency.
Cell-free plasma hemoglobin removal by dialyzers with various permeability profiles
2015-11-10

Abstract The release of hemoglobin from mechanically stressed erythrocytes into plasma is a general side effect of extracorporeal therapies, such as extracorporeal membrane oxygenation or hemodialysis. In many reported cases dialysis patients showed elevated cell-free plasma hemoglobin (CPH) levels which are associated with pathophysiological effects. In this in vitro study, the CPH clearance capacity of various filters with different permeability profiles was measured. Simulated dialysis treatments were conducted and clearance was calculated from variations in CPH concentrations over time by measuring plasma absorbance at 405 nm. Conventional high-flux filters exhibited no detectable clearance of CPH. High-flux filters with extended permeability exhibited clearances between 5.8 ± 1.2 and 12.7 ± 1.7 ml/min when tested with plasma and between 5.8 ± 1.2 and 11.3 ± 1.6 ml/min when tested with whole blood. septeX high-cutoff filters had clearances between 13.8 ± 1.8 and 15.5 ± 1.7 ml/min when tested with plasma and of 22.6 ± 2.9 ml/min when tested with whole blood. This study demonstrated that filters with extended permeability and the septeX filter enable CPH removal when used as in chronic and acute settings.
Holmium(III) Supermesityl-Imide Complexes Bearing Methylaluminato/Gallato Ligands
2015-11-10

Heterobimetallic μ2-imide complexes [Ho(μ2-Nmes*){Al(CH3)4}]2 (1, supermesityl = mes* = C6H2tBu3-2,4,6) and [Ho(μ2-Nmes*){Ga(CH3)4}]2 (2) have been synthesized from homoleptic complexes Ho[M(CH3)4]3 (M = Al, Ga) via deprotonation of H2Nmes* or with K[NH(mes*)] according to a salt metathesis-protonolysis tandem reaction. Single-crystal X-ray diffraction of isostructural complexes [Ho(μ2-Nmes*){M(CH3)4}]2 (M = Al, Ga) revealed asymmetric Ho2N2 metallacycles with very short Ho–N bond lengths and secondary Ho arene interactions.
Glycosylated Metal Phthalocyanines
2015-11-10

In the first part; the syntheses of mono-; di-; and tetra-glycosylated phthalonitriles is described; which are the most used starting materials for the preparation of the corresponding glycosylated metal (mostly zinc) phthalocyanines. In the second section; the preparation of symmetric and unsymmetric mono-; tetra-; and octa- glycosylated zinc phthalocyanines are reviewed; in which the sugar is attached to the phthalocyanine macrocycle; either anomerically or via another one of its OH-groups.
Abstract 19159: Performance of T1 Mapping Cardiac Magnetic Resonance Imaging as Compared to Biventricular Endomyocardial Biopsy in Patients With Suspected Myocarditis
2015-11-10

Background: The diagnostic performance of cardiac magnetic resonance (CMR) imaging in suspected myocarditis is still limited. Recently, CMR T1 mapping has been suggested to yield excellent diagnostic accuracies in patients with suspected myocarditis as compared to healthy controls. However, the true diagnostic performance of T1 mapping when compared to endomyocardial biopsy (EMB) in patients with a variety of pathologies is till unknown and was therefore assessed in this study. Methods and Results: Within the final analyses, 129 consecutive patients with suspected acute or chronic myocarditis were included. Patients had to fulfill indications for CMR imaging according to the JACC White consensus paper. All patients underwent biventricular EMB, cardiac catheterization for exclusion of coronary artery disease, and MRI on a 1.5 Tesla tomography (Intera, CV, Philips Medical Systems, Best, the Netherlands). The CMR protocol included standard Lake-Louise (LL) parameters as well as native and post contrast T1 mapping using a modified Look-Locker inversion recovery sequence. Patients were divided into 2 groups according to duration of symptoms: patients with acute symptoms ≤14 days and those with chronic symptoms &gt;14 days. The diagnostic performance of LL criteria, native T1 and extracellular volume fraction (ECV) is summarized in the table. In patients with acute symptoms, native T1 yielded best diagnostic performance (81%) followed by ECV (75%), whereas accuracy of LL was found to be inadequate (60%). In patients with chronic symptoms, neither imaging technique or criteria yielded sufficient diagnostic accuracies. Conclusion: In patients with acute symptoms and suspected myocarditis, T1 mapping provides a useful tool for the confirming or rejecting the diagnosis of myocarditis and is superior to LL criteria. In contrast, native T1 and extracellular volume fraction demonstrated unsatisfying diagnostic accuracies in patients with chronic symptoms.
Abstract 17607: MicroRNA Expression Profiles in Endomyocardial Biopsies From Patients With Myocarditis - Association With Left Ventricular Function and Clinical Events
2015-11-10

Background: Myocarditis represents an important cause of chronic dilated cardiomyopathy. Predicting the clinical course of patients with myocarditis is difficult and the prognostic value of current histological markers remains controversial. We tested whether expression of selected microRNAs (miRNAs) in endomyocardial biopsies is related to left ventricular (LV) function and clinical events in patients with myocarditis. Methods: Endomyocardial biopsies were obtained from patients with non-inflammatory dilated cardiomyopathy (n=22) and histologically proven myocarditis (n=81). Based on literature search, we predefined a set of 6 miRNAs implicated in inflammation (miR-155, miR-146b), heart failure (miR-21, miR-133a), endothelial cell (miR-126) and skeletal muscle function (miR-206). Expression of these miRNAs in endomyocardial biopsies was quantified by RT-PCR. Results: Expression of miR-133a, miR-206 and miR-155 was markedly upregulated in endomyocardial biopsies from patients with myocarditis as compared to patients with dilated cardiomyopathy, irrespective of viral or non-viral etiology. Levels of miR-133a (R=0,68, P&lt;0,01) and miR-155 (R=0,65, P&lt;0,01) significantly correlated with CD68 cell count in endomyocardial biopsies from patients with myocarditis. Patients with myocarditis and preserved LV function at study entry displayed higher endomyocardial expression of miR-133a than patients with reduced LV function. Higher expression levels of miR-133a were associated with improved LV function during a mean follow-up of 3,1 years. Importantly, in a Kaplan-Meier estimate, patients with myocarditis and miR-133a levels above median showed longer survival free of death and malignant arrhythmias. Conclusion: The present study demonstrates that in a predefined set of miRNAs, relevant to cardiovascular pathology, endomyocardial miR-133a levels correlate with macrophage infiltration, improved LV function and clinical outcome in a comparatively large cohort of patients with histologically proven myocarditis. miR-133a may serve as a potential novel biomarker and therapeutic target in human myocarditis.
Faster processing of moving compared to flashed bars in awake macaque V1 provides a neural correlate of the flash lag illusion
2015-11-10

Abstract When the brain has determined the position of a moving object, due to anatomical and processing delays, the object will have already moved to a new location. Given the statistical regularities present in natural motion, the brain may have acquired compensatory mechanisms to minimize the mismatch between the perceived and the real position of a moving object. A well-known visual illusion — the flash lag effect — points towards such a possibility. Although many psychophysical models have been suggested to explain this illusion, their predictions have not been tested at the neural level, particularly in a species of animal known to perceive the illusion. Towards this, we recorded neural responses to flashed and moving bars from primary visual cortex (V1) of awake, fixating macaque monkeys. We found that the response latency to moving bars of varying speed, motion direction and luminance was shorter than that to flashes, in a manner that is consistent with psychophysical results. At the level of V1, our results support the differential latency model positing that flashed and moving bars have different latencies. As we found a neural correlate of the illusion in passively fixating monkeys, our results also suggest that judging the instantaneous position of the moving bar at the time of flash — as required by the postdiction/motion-biasing model — may not be necessary for observing a neural correlate of the illusion. Our results also suggest that the brain may have evolved mechanisms to process moving stimuli faster and closer to real time compared with briefly appearing stationary stimuli. New and Noteworthy We report several observations in awake macaque V1 that provide support for the differential latency model of the flash lag illusion. We find that the equal latency of flash and moving stimuli as assumed by motion integration/postdiction models does not hold in V1. We show that in macaque V1, motion processing latency depends on stimulus luminance, speed and motion direction in a manner consistent with several psychophysical properties of the flash lag illusion.