julilili42/papers huggingface dataset:
Effects of the jimpy mutation on mouse retinal structure and function
2015-05-23

ABSTRACT The Jimpy mutant mouse has a point mutation in the proteolipid protein gene ( plp1 ). The resulting misfolding of the protein leads to oligodendrocyte death, myelin destruction, and failure to produce adequately myelinated axons in the central nervous system (CNS). It is not known how the absence of normal myelination during development influences neural function. We characterized the Jimpy mouse retina to find out whether lack of myelination in the optic nerve during development has an effect on normal functioning and morphology of the retina. Optokinetic reflex measurements showed that Jimpy mice had, in general, a functional visual system. Both PLP1 antibody staining and reverse transcriptase–polymerase chain reaction for plp1 mRNA showed that plp1 is not expressed in the wild‐type retina. However, in the optic nerve, plp1 is normally expressed, and consequently, in Jimpy mutant mice, myelination of axons in the optic nerve was mostly absent. Nevertheless, neither axon count nor axon ultrastructure in the optic nerve was affected. Physiological recordings of ganglion cell activity using microelectrode arrays revealed a decrease of stimulus‐evoked activity at mesopic light levels. Morphological analysis of the retina did not show any significant differences in the gross morphology, such as thickness of retinal layers or cell number in the inner and outer nuclear layer. The cell bodies in the inner nuclear layer, however, were larger in the peripheral retina of Jimpy mutant mice. Antibody labeling against cell type–specific markers showed that the number of rod bipolar and horizontal cells was increased in Jimpy mice. In conclusion, whereas the Jimpy mutation has dramatic effects on the myelination of retinal ganglion cell axons, it has moderate effects on retinal morphology and function. J. Comp. Neurol. 523:2788–2806, 2015. © 2015 Wiley Periodicals, Inc.
Stimulation of Suicidal Erythrocyte Death by Naphthazarin
2015-05-25

Abstract The 1,4‐naphthoquinone derivative naphthazarin may trigger apoptosis and is thus considered for the treatment of malignancy. On the other hand, naphthazarin decreases neurotoxicity. In analogy to apoptosis of nucleated cells, erythrocytes may enter eryptosis, the suicidal erythrocyte death characterized by cell shrinkage and by cell membrane scrambling with translocation of phosphatidylserine to the erythrocyte surface. Signalling leading to triggering of eryptosis include increase in cytosolic Ca 2+ ‐activity ([Ca 2+ ] i ), ceramide and oxidative stress. The present study explored whether naphthazarin impacts on eryptosis and, if so, to unravel underlying mechanisms. To this end, erythrocyte volume was estimated from forward scatter, phosphatidylserine abundance at the erythrocyte surface from FITC ‐annexin‐V‐binding, [Ca 2+ ] i from Fluo3 fluorescence, reactive oxidant species ( ROS ) from 2′,7′‐dichlorodihydrofluorescein diacetate ( DCFDA ) fluorescence and ceramide abundance at the erythrocyte surface from binding of fluorescent antibodies in flow cytometry. As a result, a 24‐hr exposure of human erythrocytes to naphthazarin (10 μ m ) significantly decreased erythrocyte forward scatter, significantly increased the percentage of annexin‐V‐binding cells, significantly increased ceramide abundance at the erythrocyte surface and significantly increased ROS . The effect of naphthazarin on annexin‐V‐binding was not significantly blunted by removal of extracellular Ca 2+ . In conclusion, naphthazarin stimulates eryptosis, an effect at least in part due to oxidative stress and enhanced ceramide abundance at the erythrocyte surface.
Construction of an Internally B3N3‐Doped Nanographene Molecule
2015-05-26

Abstract The synthesis of a hexa‐ peri ‐hexabenzocoronene (HBC) with a central borazine core is described. The solid‐state structure of this BN‐doped HBC (BN‐HBC) is isotypic with that of the parent HBC. Scanning tunneling microscopy shows that BN‐HBC lies flat on Au(111) in a two‐dimensional pattern.
Comparison of Atomic Force Microscopy and Scanning Ion Conductance Microscopy for Live Cell Imaging
2015-05-26

Atomic force microscopy (AFM) and scanning ion conductance microscopy (SICM) are excellent and commonly used techniques for imaging the topography of living cells with high resolution. We present a direct comparison of AFM and SICM for imaging microvilli, which are small features on the surface of living cells, and for imaging the shape of whole cells. The imaging quality on microvilli increased significantly after cell fixation for AFM, whereas for SICM it remained constant. The apparent shape of whole cells in the case of AFM depended on the imaging force, which deformed the cell. In the case of SICM, cell deformations were avoided, owing to the contact-free imaging mechanism. We estimated that the lateral resolution on living cells is limited by the cell's elastic modulus for AFM, while it is not for SICM. By long-term, time-lapse imaging of microvilli dynamics, we showed that the imaging quality decreased with time for AFM, while it remained constant for SICM.
Excretion of cytoplasmic proteins (ECP) in Staphylococcus aureus
2015-05-26

Summary E xcretion of c ytoplasmic p roteins ( ECP ) is a common physiological feature in bacteria and eukaryotes. However, how these proteins without a typical signal peptide are excreted in bacteria is poorly understood. We studied the excretion pattern of cytoplasmic proteins using two glycolytic model enzymes, aldolase and enolase, and show that their excretion takes place mainly during the exponential growth phase in S taphylococcus aureus very similar to that of S bi, an IgG ‐binding protein, which is secreted via the S ec‐pathway. The amount of excreted enolase is substantial and is comparable with that of S bi. For localization of the exit site, we fused aldolase and enolase with the peptidoglycan‐binding motif, LysM , to trap the enzymes at the cell wall. With both immune fluorescence labeling and immunogold localization on electron microscopic thin sections aldolase and enolase were found apart from the cytoplasmic area particularly in the cross wall and at the septal cleft of dividing cells, whereas the non‐excreted N dh2, a soluble NADH :quinone oxidoreductase, is only seen attached to the inner side of the cytoplasmic membrane. The selectivity, the timing and the localization suggest that ECP is not a result of unspecific cell lysis but is mediated by an as yet unknown mechanism.
The Fans’ Perception of Competitive Balance and Its Impact on Willingness-to-Pay for a Single Game
2015-05-26

The economics literature related to the uncertainty of outcome hypothesis reopens the discussion of whether the fans’ perceptions of competitive balance (CB) are in line with Rottenberg’s and Neale’s theory. This article contributes to the literature by analyzing the effect of fans’ perceptions of suspensefulness on their willingness-to-pay for a single-game ticket and evaluating monetarily the (un)importance of CB. Results suggest that fans’ notions of competitiveness influence their spending behavior, rising as perceived balance rises, at least up to high levels of competitiveness.
Distinct Spacing Between Anionic Groups: An Essential Chemical Determinant for Achieving Thiophene‐Based Ligands to Distinguish β‐Amyloid or Tau Polymorphic Aggregates
2015-05-26

Abstract The accumulation of protein aggregates is associated with many devastating neurodegenerative diseases and the existence of distinct aggregated morphotypes has been suggested to explain the heterogeneous phenotype reported for these diseases. Thus, the development of molecular probes able to distinguish such morphotypes is essential. We report an anionic tetrameric oligothiophene compound that can be utilized for spectral assignment of different morphotypes of β‐amyloid or tau aggregates present in transgenic mice at distinct ages. The ability of the ligand to spectrally distinguish between the aggregated morphotypes was reduced when the spacing between the anionic substituents along the conjugated thiophene backbone was altered, which verified that specific molecular interactions between the ligand and the protein aggregate are necessary to detect aggregate polymorphism. Our findings provide the structural and functional basis for the development of new fluorescent ligands that can distinguish between different morphotypes of protein aggregates.
Dynamics of Suspended and Attached Aerobic Toluene Degraders in Small-Scale Flow-through Sediment Systems under Growth and Starvation Conditions
2015-05-26

The microbially mediated reactions, that are responsible for field-scale natural attenuation of organic pollutants, are governed by the concurrent presence of a degrading microbial community, suitable energy and carbon sources, electron acceptors, as well as nutrients. The temporal lack of one of these essential components for microbial activity, arising from transient environmental conditions, might potentially impair in situ biodegradation. This study presents results of small scale flow-through experiments aimed at ascertaining the effects of substrate-starvation periods on the aerobic degradation of toluene by Pseudomonas putida F1. During the course of the experiments, concentrations of attached and mobile bacteria, as well as toluene and oxygen were monitored. Results from a fitted reactive-transport model, along with the observed profiles, show the ability of attached cells to survive substrate-starvation periods of up to four months and suggest a highly dynamic exchange between attached and mobile cells under growth conditions and negligible cell detachment under substrate-starvation conditions. Upon reinstatement of toluene, it was readily degraded without a significant lag period, even after a starvation period of 130 days. Our experimental and modeling results strongly suggest that aerobic biodegradation of BTEX-hydrocarbons at contaminated field sites is not hampered by intermittent starvation periods of up to four months.
Combined unsupervised–supervised classification of multiparametric PET/MRI data: application to prostate cancer
2015-05-26

Multiparametric medical imaging data can be large and are often complex. Machine learning algorithms can assist in image interpretation when reliable training data exist. In most cases, however, knowledge about ground truth (e.g. histology) and thus training data is limited, which makes application of machine learning algorithms difficult. The purpose of this study was to design and implement a learning algorithm for classification of multidimensional medical imaging data that is robust and accurate even with limited prior knowledge and that allows for generalization and application to unseen data. Local prostate cancer was chosen as a model for application and validation. 16 patients underwent combined simultaneous [ 11 C]‐choline positron emission tomography (PET)/MRI. The following imaging parameters were acquired: T 2 signal intensities, apparent diffusion coefficients, parameters K trans and K ep from dynamic contrast‐enhanced MRI, and PET standardized uptake values (SUVs). A spatially constrained fuzzy c ‐means algorithm (sFCM) was applied to the single datasets and the resulting labeled data were used for training of a support vector machine (SVM) classifier. Accuracy and false positive and false negative rates of the proposed algorithm were determined in comparison with manual tumor delineation. For five of the 16 patients rates were also determined in comparison with the histopathological standard of reference. The combined sFCM/SVM algorithm proposed in this study revealed reliable classification results consistent with the histopathological reference standard and comparable to those of manual tumor delineation. sFCM/SVM generally performed better than unsupervised sFCM alone. We observed an improvement in accuracy with increasing number of imaging parameters used for clustering and SVM training. In particular, including PET SUVs as an additional parameter markedly improved classification results. A variety of applications are conceivable, especially for imaging of tissues without easily available histopathological correlation. Copyright © 2015 John Wiley &amp; Sons, Ltd.
Therapeutic potential of manipulating suicidal erythrocyte death
2015-05-26

In theory, anemia due to excessive eryptosis could be alleviated by treatment with small molecules inhibiting eryptosis. In malaria, stimulators of eryptosis may accelerate death of infected erythrocytes and thus favorably influence the clinical course of the disease. Many small molecules inhibit or stimulate eryptosis. Several stimulators favorably influence murine malaria. Further preclinical and subsequent clinical studies are required to elucidate the therapeutic potential of stimulators or inhibitors of eryptosis.
Identification of a new order of root-colonising fungi in the Entorrhizomycota: Talbotiomycetales ord. nov. on eudicotyledons
2015-05-26

The recently described fungal phylum Entorrhizomycota was established solely for the genus Entorrhiza, species of which cause root-galls in Cyperaceae and Juncaceae. Talbotiomyces calosporus (incertae sedis) shares morphological characteristics and an ecological niche with species of Entorrhiza. We investigated the higher classification of T. calosporus to determine whether it belongs in Entorrhizomycota. Ribosomal DNA sequences showed Talbotiomyces to be a close relative of Entorrhiza and both taxa form a highly supported monophyletic group. Based on molecular phylogenetic analyses and in congruence with existing morphological and ecological data, Entorrhiza and Talbotiomyces represent a deep dichotomy within the Entorrhizomycota. While species of Entorrhiza are characterised by dolipores and occur on monocotyledons, members of Talbotiomyces are characterised by simple pores and are associated with eudicotyledons. This expands the host range of the recently described Entorrhizomycota from Poales to other angiosperms. Higher taxa, namely Talbotiomycetales ord. nov. and Talbotiomycetaceae fam. nov., are proposed here to accommodate Talbotiomyces.
Prometabolites of 5‐Diphospho‐myo‐inositol Pentakisphosphate
2015-05-26

Abstract Diphospho‐ myo ‐inositol phosphates (PP‐InsP y ) are an important class of cellular messengers. Thus far, no method for the transport of PP‐InsP y into living cells is available. Owing to their high negative charge density, PP‐InsP y will not cross the cell membrane. A strategy to circumvent this issue involves the generation of precursors in which the negative charges are masked with biolabile groups. A PP‐InsP y prometabolite would require twelve to thirteen biolabile groups, which need to be cleaved by cellular enzymes to release the parent molecules. Such densely modified prometabolites of phosphate esters and anhydrides have never been reported to date. This study discloses the synthesis of such agents and an analysis of their metabolism in tissue homogenates by gel electrophoresis. The acetoxybenzyl‐protected system is capable of releasing 5‐PP‐InsP 5 in mammalian cell/tissue homogenates within a few minutes and can be used to release 5‐PP‐InsP 5 inside cells. These molecules will serve as a platform for the development of fundamental tools required to study PP‐InsP y physiology.
Flow through Experiment on CO2-brine-rock Interaction in a Sandstone from the Altmark Gas Reservoir
2015-05-26

Summary We performed flow through experiments to study the water-rock interactions caused by CO2 injection in sandstones obtained from the Altmark natural gas reservoir under reservoir conditions of 125°C and 50 bar CO2 partial pressure. CO2-saturated brine (41.62 g/ L NaCl and 31.98 g/L CaCl2•2H2O), mimicking the chemical composition of the formation water, was used as an injection solution. The major components in the sandstone were quartz (clasts + cement), feldspars, clay minerals (illite and chlorite), and anhydrite, the latter present mostly as cement. Trace amounts of carbonate and barite cements were also present. Fluid analysis suggested the predominant dissolution of anhydrite causing increased concentrations of sulfate at early time periods. Dissolution of feldspar, barite and minor amounts of clay (illite + chlorite) was also evident during the flow-through experiment. Geochemical modeling does not predict secondary mineral precipitation under these conditions. The experimental data could be used for numerical simulations predicting CO2 storage during injection in sandstone reservoirs.
A Testbed Combining Visual Perception Models for Geographic Gaze Contingent Displays
2015-05-26

We present a testbed featuring gaze-contingent displays (GCDs), in which we combined multiple models of the human visual system (HVS) to manage the visual level of detail. GCDs respond to the viewer's gaze in real-time, rendering a space-variant visualization. Our testbed is optimized for testing mathematical models of the human visual perception utilized in GCDs. Specifically, we combined models of contrast sensitivity, color perception and depth of field; and customized our implementation for geographic imagery. In this customization process, similarly to the geographic information systems (GIS), we georeference the input images, add vector layers on demand, and enable stereo viewing. After the implementation, we studied the computational and perceptual benefits of the studied perceptual models in terms of data reduction and user experience in geographic information science (GIScience) domain. Our computational validation experiments and the user study results indicate the HVS-based data reduction solutions are competitive, and encourage further research. We believe the research outcome and the testbed will be relevant in domains where visual interpretation of imagery is a part of professional life; such as in search and rescue, damage assessment in hazards, geographic image interpretation or urban planning.
Revisiting Sphere Sovereignty to Interpret Restrictions on Religious Freedom
2015-05-26

In this article, the Kuyperian concept of sphere sovereignty will be revisited in order to describe the multidimensionality of religious freedom. This article will show that true religious freedom requires not only a sovereign church sphere – the respect of church autonomy –, but also the freedom for religious expression in all other spheres of society. The first section will try to show that restrictions on religious expression in any sphere of society are restrictions on religious freedom. The second and third sections will provide examples of two global dynamics which in very distinct ways go against sphere sovereignty and specifically restrict religious expression in different spheres of society: “Islamic extremism” and “secular intolerance”. The article will conclude with a reflection about the virtues of sphere sovereignty as a guarantee against tyranny, and therefore also as a safeguard of religious freedom.
Performance of T1 and T2 Mapping Cardiovascular Magnetic Resonance to Detect Active Myocarditis in Patients With Recent-Onset Heart Failure
2015-05-27

Background— This study evaluated the performance of novel quantitative T1 and T2 mapping cardiovascular magnetic resonance (CMR) techniques to identify active myocarditis in patients with recent-onset heart failure. Methods and Results— Thirty-one consecutive patients with recent-onset heart failure, reduced left ventricular function and clinically suspected myocarditis underwent endomyocardial biopsy and CMR at 1.5 Tesla. The CMR protocol included standard Lake-Louise parameters as well as T1 mapping using a modified Look-Locker inversion recovery sequence and T2 mapping using a hybrid gradient and spin-echo sequence. Short-axis maps were generated using an OsiriX plug-in to calculate global myocardial T1, T2, and extracellular volume fraction. Active myocarditis was defined by ongoing inflammation on endomyocardial biopsy. Endomyocardial biopsy revealed active myocarditis in 16 (52%) of 31 patients. Neither clinical characteristics, standard Lake-Louise CMR parameters, global myocardial T1 nor extracellular volume fraction differed significantly between patients with and without active myocarditis. However, median global myocardial T2 was significantly higher in patients with active myocarditis (65 ms [Q1–Q3, 61–70 ms]) than in patients without active myocarditis (59 ms [Q1–Q3, 55–64 ms]; P &lt;0.01). A cutoff value for global myocardial T2 of ≥60 ms provided a sensitivity, specificity, accuracy, negative and positive predictive value of 94% (70%–100%), 60% (32%–84%), 77% (60%–89%), 90% (56%–100%), and 71% (48%–89%) for active myocarditis, respectively. Conclusions— T2 mapping seems to be superior when compared with standard CMR parameters, global myocardial T1, and extracellular volume fraction values for assessing the activity of myocarditis in patients with recent-onset heart failure and reduced left ventricular function.
Cerebral β-Amyloidosis in Mice Investigated by Ultramicroscopy
2015-05-27

Alzheimer ́s disease (AD) is the most common neurodegenerative disorder. AD neuropathology is characterized by intracellular neurofibrillary tangles and extracellular β-amyloid deposits in the brain. To elucidate the complexity of AD pathogenesis a variety of transgenic mouse models have been generated. An ideal imaging system for monitoring β-amyloid plaque deposition in the brain of these animals should allow 3D-reconstructions of β-amyloid plaques via a single scan of an uncropped brain. Ultramicroscopy makes this possible by replacing mechanical slicing in standard histology by optical sectioning. It allows a time efficient analysis of the amyloid plaque distribution in the entire mouse brain with 3D cellular resolution. We herein labeled β-amyloid deposits in a transgenic mouse model of cerebral β-amyloidosis (APPPS1 transgenic mice) with two intraperitoneal injections of the amyloid-binding fluorescent dye methoxy-X04. Upon postmortem analysis the total number of β-amyloid plaques, the β-amyloid load (volume percent) and the amyloid plaque size distributions were measured in the frontal cortex of two age groups (2.5 versus 7-8.5 month old mice). Applying ultramicroscopy we found in a proof-of-principle study that the number of β-amyloid plaques increases with age. In our experiments we further observed an increase of large plaques in the older age group of mice. We demonstrate that ultramicroscopy is a fast, and accurate analysis technique for studying β-amyloid lesions in transgenic mice allowing the 3D staging of β-amyloid plaque development. This in turn is the basis to study neural network degeneration upon cerebral β-amyloidosis and to assess Aβ-targeting therapeutics.