julilili42/papers huggingface dataset:
Self-Regulation of Anterior Insula with Real-Time fMRI and Its Behavioral Effects in Obsessive-Compulsive Disorder: A Feasibility Study
2015-08-24

Although preliminary, results of this study confirmed that insula down-regulation is possible in patients suffering from OCD, and that volitional decreases of insula activation could be used for symptom alleviation in this disorder.
High‐resolution mapping of neuronal activation with balanced SSFP at 9.4 tesla
2015-08-24

Purpose This work investigates the feasibility of high‐resolution functional imaging of the human brain using passband balanced steady state free precession (SSFP) at 9.4 Tesla (T). To this end, the temporal signal stability, blood‐oxygen‐level‐dependent (BOLD)‐related signal changes and sensitivity to frequency offsets were evaluated. Methods Three‐dimensional slab selective and nonselective balanced SSFP have been implemented with minimized repetition time and high temporal resolution using parallel imaging, partial Fourier acquisition and elliptical scanning. Using a volume repetition time of approximately 3 s, a visual checker board stimulation was applied for 6 min. Temporal signal stability of balanced SSFP and BOLD response‐related signal changes and sensitivity to frequency changes were evaluated. Results Activation could be detected in all volunteers with BOLD‐related signal changes from 3% to 6%. At 1 mm isotropic resolution, the thermal noise SNR 0 was 67 and the total temporal noise variation tSNR was 45 supporting a very high signal stability of balanced SSFP. No significant changes of activation at different offresonance frequencies were detected. Conclusion High spatial and temporal resolution balanced SSFP at 9.4T to detect functional activation is feasible. Activation patterns and signal changes are stable and reproducible across subjects within the visual cortex, and comparable to reported values of SE‐EPI at 7T and 9.4T. Magn Reson Med 76:163–171, 2016. © 2015 Wiley Periodicals, Inc.
Trichodysplasia spinulosa-Associated Polyomavirus Uses a Displaced Binding Site on VP1 to Engage Sialylated Glycolipids
2015-08-24

Trichodysplasia spinulosa-associated Polyomavirus (TSPyV) was isolated from a patient suffering from trichodysplasia spinulosa, a skin disease that can appear in severely immunocompromised patients. While TSPyV is one of the five members of the polyomavirus family that are directly linked to a human disease, details about molecular recognition events, the viral entry pathway, and intracellular trafficking events during TSPyV infection remain unknown. Here we have used a structure-function approach to shed light on the first steps of TSPyV infection. We established by cell binding and pseudovirus infection studies that TSPyV interacts with sialic acids during attachment and/or entry. Subsequently, we solved high-resolution X-ray structures of the major capsid protein VP1 of TSPyV in complex with three different glycans, the branched GM1 glycan, and the linear trisaccharides α2,3- and α2,6-sialyllactose. The terminal sialic acid of all three glycans is engaged in a unique binding site on TSPyV VP1, which is positioned about 18 Å from established sialic acid binding sites of other polyomaviruses. Structure-based mutagenesis of sialic acid-binding residues leads to reduction in cell attachment and pseudovirus infection, demonstrating the physiological relevance of the TSPyV VP1-glycan interaction. Furthermore, treatments of cells with inhibitors of N-, O-linked glycosylation, and glycosphingolipid synthesis suggest that glycolipids play an important role during TSPyV infection. Our findings elucidate the first molecular recognition events of cellular infection with TSPyV and demonstrate that receptor recognition by polyomaviruses is highly variable not only in interactions with sialic acid itself, but also in the location of the binding site.
A general ansatz for constructing quasi-diabatic states in electronically excited aggregated systems
2015-08-24

We present a general method for analyzing the character of singly excited states in terms of charge transfer (CT) and locally excited (LE) configurations. The analysis is formulated for configuration interaction singles (CIS) singly excited wave functions of aggregate systems. It also approximately works for the second-order approximate coupled cluster singles and doubles and the second-order algebraic-diagrammatic construction methods [CC2 and ADC(2)]. The analysis method not only generates a weight of each character for an excited state, but also allows to define the related quasi-diabatic states and corresponding coupling matrix elements. In the character analysis approach, we divide the target system into domains and use a modified Pipek-Mezey algorithm to localize the canonical MOs on each domain, respectively. The CIS wavefunction is then transformed into the localized basis, which allows us to partition the wavefunction into LE configurations within domains and CT configuration between pairs of different domains. Quasi-diabatic states are then obtained by mixing excited states subject to the condition of maximizing the weight of one single LE or CT configuration (localization in configuration space). Different aims of such a procedure are discussed, either the construction of pure LE and CT states for analysis purposes (by including a large number of excited states) or the construction of effective models for dynamics calculations (by including a restricted number of excited states). Applications are given to LE/CT mixing in π-stacked systems, charge-recombination matrix elements in a hetero-dimer, and excitonic couplings in multi-chromophoric systems.
Triggering of Erythrocyte Death by Triparanol
2015-08-24

The cholesterol synthesis inhibitor Triparanol has been shown to trigger apoptosis in several malignancies. Similar to the apoptosis of nucleated cells, erythrocytes may enter eryptosis, the suicidal death characterized by cell shrinkage and cell membrane scrambling with phosphatidylserine translocation to the erythrocyte surface. Triggers of eryptosis include oxidative stress which may activate erythrocytic Ca2+ permeable unselective cation channels with subsequent Ca2+ entry and increase of cytosolic Ca2+ activity ([Ca2+]i). The present study explored whether and how Triparanol induces eryptosis. To this end, phosphatidylserine exposure at the cell surface was estimated from annexin-V-binding, cell volume from forward scatter, hemolysis from hemoglobin release, [Ca2+]i from Fluo3-fluorescence, and ROS formation from 2’,7’-dichlorodihydrofluorescein diacetate (DCFDA) dependent fluorescence. As a result, a 48 h exposure of human erythrocytes to Triparanol (20 μM) significantly increased DCFDA fluorescence and significantly increased Fluo3-fluorescence. Triparanol (15 μM) significantly increased the percentage of annexin-V-binding cells, and significantly decreased the forward scatter. The effect of Triparanol on annexin-V-binding was significantly blunted, but not abolished by removal of extracellular Ca2+. In conclusion, Triparanol leads to eryptosis, the suicidal erythrocyte death characterized by cell shrinkage and phospholipid scrambling of the erythrocyte cell membrane. Triparanol is at least in part effective by stimulating ROS formation and Ca2+ entry.
starbench: the D-type expansion of an H ii region
2015-08-25

StarBench is a project focused on benchmarking and validating different\\nstar-formation and stellar feedback codes. In this first StarBench paper we\\nperform a comparison study of the D-type expansion of an HII region. The aim of\\nthis work is to understand the differences observed between the twelve\\nparticipating numerical codes against the various analytical expressions\\nexamining the D-type phase of HII region expansion. To do this, we propose two\\nwell-defined tests which are tackled by 1D and 3D grid- and SPH- based codes.\\nThe first test examines the `early phase' D-type scenario during which the\\nmechanical pressure driving the expansion is significantly larger than the\\nthermal pressure of the neutral medium. The second test examines the `late\\nphase' D-type scenario during which the system relaxes to pressure equilibrium\\nwith the external medium. Although they are mutually in excellent agreement,\\nall twelve participating codes follow a modified expansion law that deviates\\nsignificantly from the classical Spitzer solution in both scenarios. We present\\na semi-empirical formula combining the two different solutions appropriate to\\nboth early and late phases that agrees with high-resolution simulations to\\n . This formula provides a much better benchmark solution for code\\nvalidation than the Spitzer solution. The present comparison has validated the\\nparticipating codes and through this project we provide a dataset for\\ncalibrating the treatment of ionizing radiation hydrodynamics codes.\\n
Phenotypic heterogeneity and temporal expression of the capsular polysaccharide in Staphylococcus aureus
2015-08-25

Summary Bacteria respond to ever‐changing environments through several adaptive strategies. This includes mechanisms leading to a high degree of phenotypic variability within a genetically homogeneous population. In S taphylococcus aureus , the capsular polysaccharide ( CP ) protects against phagocytosis, but also impedes adherence to endothelial cells and/or matrix proteins. We analysed the regulation of core biosynthesis genes ( capA‐ P ) necessary for CP synthesis using single‐cell assays (immunofluorescence and promoter‐activity). In persistent human carriers, we found a distinct subpopulation of nasal S . aureus to be CP positive. In vitro , cap expression is also heterogeneous and strongly growth‐phase dependent. We asked whether this peculiar expression pattern (earlyOff/lateHeterogen) is orchestrated by the quorum system A gr. We show that the A gr‐driven effector molecule RNAIII promotes cap expression largely via inactivation of the repressor R ot. High NaCl , deletion of CodY or Sae also resulted in higher cap expression but did not change the earlyOFF/lateHeterogen expression pattern. Activity of the quorum system itself is largely homogenous and does not account for the observed heterogeneity of cap expression or the strictly growth phase dependent expression. Our findings are in contrast to the prevailing view that quorum sensing is the main driving force for virulence gene expression when bacterial cell densities increase.
Structure Learning in Bayesian Sensorimotor Integration
2015-08-25

Previous studies have shown that sensorimotor processing can often be described by Bayesian learning, in particular the integration of prior and feedback information depending on its degree of reliability. Here we test the hypothesis that the integration process itself can be tuned to the statistical structure of the environment. We exposed human participants to a reaching task in a three-dimensional virtual reality environment where we could displace the visual feedback of their hand position in a two dimensional plane. When introducing statistical structure between the two dimensions of the displacement, we found that over the course of several days participants adapted their feedback integration process in order to exploit this structure for performance improvement. In control experiments we found that this adaptation process critically depended on performance feedback and could not be induced by verbal instructions. Our results suggest that structural learning is an important meta-learning component of Bayesian sensorimotor integration.
Testing the role of luminance edges in White's illusion with contour adaptation
2015-08-25

White's illusion is the perceptual effect that two equiluminant gray patches superimposed on a black-and-white square-wave grating appear different in lightness: A test patch placed on a dark stripe of the grating looks lighter than one placed on a light stripe. Although the effect does not depend on the aspect ratio of the test patches, and thus on the amount of border that is shared with either the dark or the light stripe, the context of each patch must, in a yet to be specified way, influence their lightness. We employed a contour adaptation paradigm (Anstis, 2013) to test the contribution of each of the test patches' edges to the perceived lightness of the test patches. We found that adapting to the edges that are oriented parallel to the grating slightly increased the lightness illusion, whereas adapting to the orthogonal edges abolished, or for some observers even reversed, the lightness illusion. We implemented a temporal adaptation mechanism in three spatial filtering models of lightness perception, and show that the models cannot account for the observed adaptation effects. We conclude that White's illusion is largely determined by edge contrast across the edge orthogonal to the grating, whereas the parallel edge has little or no influence. We suggest mechanisms that could explain this asymmetry.
Porcine survival model to simulate acute upper gastrointestinal bleedings
2015-08-25

The existing animal models used for the simulation of acute gastrointestinal bleedings are usually non-survival models. We developed and evaluated a new porcine model (domestic pig, German Landrace) in which the animal remains alive and survives the artificial bleeding without any cardiovascular impairment. This consists of a bleeding catheter which is implanted into the stomach, then subcutaneously tunnelled from the abdomen to the neck where it is exteriorized and fixed with sutures. Using the injection of porcine blood, controllable and reproducible acute upper gastrointestinal bleeding can be simulated while maintaining normal gastrointestinal motility and physiology. Depending on the volume of blood applied through the gastric catheter, the bleeding intensity can be varied from traces of blood to a massive haemorrhage. This porcine model could be valuable, e.g. for testing the efficacy of new bleeding diagnostics in large animals before human use.
Comprehensive Oncologic Imaging in Infants and Preschool Children With Substantially Reduced Radiation Exposure Using Combined Simultaneous 18F-Fluorodeoxyglucose Positron Emission Tomography/Magnetic Resonance Imaging
2015-08-26

FDG PET/MRI is at least equivalent to FDG PET/CT for oncologic imaging in young children. Specifically, superior soft tissue contrast of MRI results in higher confidence in lesion interpretation. Substantial savings in radiation exposure can be achieved, and the number of necessary imaging examinations can be reduced using PET/MRI compared with PET/CT.
Evolution of circumbinary planets around eccentric binaries: The case of Kepler-34
2015-08-26

\\n The existence of planets orbiting a central binary star system immediately raises questions regarding their formation and dynamical evolution. Recent discoveries of circumbinary planets by the Kepler space telescope has shown that some of these planets reside close to the dynamical stability limit where the strong perturbations induced by the binary makes it very difficult to form planets in situ. For binary systems with nearly circular orbits, such as Kepler-38, the observed proximity of planetary orbits to the stability limit can be understood by an evolutionary process in which planets form farther out in the calmer environment of the disk and migrate in toward their observed position. The Kepler-34 system is different from other systems because it has a high orbital eccentricity of 0.52. We analyzed evolutionary scenarios for the planet observed around this system using two-dimensional hydrodynamical simulations. The highly eccentric binary opens a wide inner hole in the disk that is also eccentric and displays a slow prograde precession. As a result of the large eccentric inner gap, an embedded planet settles in a final equilibrium position that lies beyond the observed location of Kepler-34 b, but has the correct eccentricity. In this configuration, the planetary orbit is aligned with the disk in a state of apsidal corotation. To account for the closer orbit of Kepler-34 b to the central binary, we considered a two-planet scenario and examined the evolution of the system through joint inward migration and capture into mean-motion resonances. When the inner planet orbits inside the gap of the disk, planet-planet scattering ensues. While often one object is thrown into a large, highly eccentric orbit, the system is at times left with a planet close to the observed orbit, suggesting that Kepler-34 might have had two circumbinary planets where one might have been scattered out of the system or into an orbit where it did not transit the central binary during the operation of Kepler. \\n
SLy1 regulates T‐cell proliferation during Listeria monocytogenes infection in a Foxo1‐dependent manner
2015-08-26

Infection of mice with Listeria monocytogenes results in a strong T‐cell response that is critical for an efficient defense. Here, we demonstrate that the adapter protein SLy1 (SH3‐domain protein expressed in Lymphocytes 1) is essential for the generation of a fully functional T‐cell response. The lack of SLy1 leads to reduced survival rates of infected mice. The increased susceptibility of SLy1 knock‐out (KO) mice was caused by reduced proliferation of differentiated T cells. Ex vivo analyses of isolated SLy1 KO T cells displayed a dysregulation of Forkhead box protein O1 shuttling after TCR signaling, which resulted in an increased expression of cell cycle inhibiting genes, and therefore, reduced expansion of the T‐cell population. Forkhead box protein O1 shuttles to the cytoplasm after phosphorylation in a protein complex including 14‐3‐3 proteins. Interestingly, we observed a similar regulation for the adapter protein SLy1, where TCR stimulation results in SLy1 phosphorylation and SLy1 export to the cytoplasm. Moreover, immunoprecipitation analyses revealed a binding of SLy1 to 14‐3‐3 proteins. Altogether, this study describes SLy1 as an immunoregulatory protein, which is involved in the generation of adaptive immune responses during L. monocytogenes infection, and provides a model of how SLy1 regulates T‐cell proliferation.
Contrast Gradient-Based Blood Velocimetry With Computed Tomography
2015-08-26

The new theoretical framework increases the understanding of the relationship between the blood velocity, CT acquisition velocity, and iodine contrast enhancement in CT images, and it interconnects existing blood velocimetry methods with research on transluminary attenuation gradients. With these new insights, novel strategies for CT blood velocimetry, such as the contrast gradient-based method presented in this article, may be developed.
Automatic refunctionalization to a language with copattern matching: with applications to the expression problem
2015-08-26

Defunctionalization and refunctionalization establish a correspondence between first-class functions and pattern matching, but the correspondence is not symmetric: Not all uses of pattern matching can be automatically refunctionalized to uses of higher-order functions. To remedy this asymmetry, we generalize from first-class functions to arbitrary codata. This leads us to full defunctionalization and refunctionalization between a codata language based on copattern matching and a data language based on pattern matching. We observe how programs can be written as matrices so that they are modularly extensible in one dimension but not the other. In this representation, defunctionalization and refunctionalization correspond to matrix transposition which effectively changes the dimension of extensibility a program supports. This suggests applications to the expression problem.
Polarization-dependent single-molecule spectroscopy on photosystem I
2015-08-26

Single-molecule spectroscopy (SMS) at low temperature was used to study the spectral properties, heterogeneities and spectral dynamics of the chlorophyll a (Chl a) molecules responsible for the fluorescence emission of photosystem I (PS I). The fluorescence spectra of single PS I complexes are dominated by several red-shifted Chl a molecules categorized into red pools called C708 and C719. By polarization dependent measurements we demonstrate spectrally separate emissions corresponding to C708 and C719 in single PS I monomers and trimers. Moreover, we compared the results of SMS polarization dependent between monomeric and trimeric PS I complexes and give an estimation for the orientation between these red pools. As a consequence, we get new insight into the energy transfer towards and between the red Chl a molecules in PS I complexes.
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways
2015-08-27

Escher is a web application for visualizing data on biological pathways. Three key features make Escher a uniquely effective tool for pathway visualization. First, users can rapidly design new pathway maps. Escher provides pathway suggestions based on user data and genome-scale models, so users can draw pathways in a semi-automated way. Second, users can visualize data related to genes or proteins on the associated reactions and pathways, using rules that define which enzymes catalyze each reaction. Thus, users can identify trends in common genomic data types (e.g. RNA-Seq, proteomics, ChIP)--in conjunction with metabolite- and reaction-oriented data types (e.g. metabolomics, fluxomics). Third, Escher harnesses the strengths of web technologies (SVG, D3, developer tools) so that visualizations can be rapidly adapted, extended, shared, and embedded. This paper provides examples of each of these features and explains how the development approach used for Escher can be used to guide the development of future visualization tools.
Current diagnosis and treatment of basal cell carcinoma
2015-08-27

Summary Basal cell carcinoma represents is most common tumor in fair‐skinned individuals. In Germany, age‐standardized incidence rates are 63 (women) and 80 (men) per 100,000 population per year. Early lesions may be difficult to diagnose merely on clinical grounds. Here, noninvasive diagnostic tools such as optical coherence tomography and confocal laser scanning microscopy may be helpful. The clinical diagnosis is usually confirmed by histology. Standard therapy consists of complete excision with thorough histological examination, either by means of micrographic surgery or, depending on tumor size and location as well as infiltration, using surgical margins of 3–5 mm or more. In particular, multiple basal cell carcinomas (such as in Gorlin‐Goltz syndrome) and locally advanced as well as rarely also metastatic basal cell carcinoma may pose a therapeutic challenge. In superficial basal cell carcinoma, nonsurgical therapies such as photodynamic therapy or topical agents may be considered. In case of locally advanced or metastatic basal cell carcinoma, an interdisciplinary tumor board should issue therapeutic recommendations. These include radiation therapy as well as systemic therapy with a hedgehog inhibitor.