julilili42/papers huggingface dataset:
The Vicious Cycle of Family Atmosphere, Interpersonal Self-concepts, and Paranoia in Schizophrenia—A Longitudinal Study
2015-04-29

Recent cognitive models of paranoid delusions highlight the role of self-concepts in the development and maintenance of paranoia. Evidence is growing that especially interpersonal self-concepts are relevant in the genesis of paranoia. In addition, negative interpersonal life-experiences are supposed to influence the course of paranoia. As dysfunctional family atmosphere corresponds with multiple distressing dyadic experiences, it could be a risk factor for the development and maintenance of paranoia. A total of 160 patients with a diagnosis of schizophrenia were assessed twice within 12 months. Standardized questionnaires and symptom rating scales were used to measure interpersonal self-concepts, perceived family atmosphere, and paranoia. Data were analyzed using longitudinal cross-lagged structural equation models. Perceived negative family atmosphere was associated with the development of more pronounced negative interpersonal self-concepts 12 months later. Moreover, paranoia was related to negative family atmosphere after 12 months as well. As tests revealed that reversed associations were not able to explain the data, we found evidence for a vicious cycle between paranoia, family atmosphere, and interpersonal self-concepts as suggested by theoretical/cognitive model of paranoid delusions. Results suggest that broader interventions for patients and their caretakers that aim at improving family atmosphere might also be able to improve negative self-concepts and paranoia.
Electronic damage in S atoms in a native protein crystal induced by an intense X-ray free-electron laser pulse
2015-04-29

Current hard X-ray free-electron laser (XFEL) sources can deliver doses to biological macromolecules well exceeding 1 GGy, in timescales of a few tens of femtoseconds. During the pulse, photoionization can reach the point of saturation in which certain atomic species in the sample lose most of their electrons. This electronic radiation damage causes the atomic scattering factors to change, affecting, in particular, the heavy atoms, due to their higher photoabsorption cross sections. Here, it is shown that experimental serial femtosecond crystallography data collected with an extremely bright XFEL source exhibit a reduction of the effective scattering power of the sulfur atoms in a native protein. Quantitative methods are developed to retrieve information on the effective ionization of the damaged atomic species from experimental data, and the implications of utilizing new phasing methods which can take advantage of this localized radiation damage are discussed.
3D hydrodynamic interactions lead to divergences in 2D diffusion
2015-04-29

We investigate the influence of 3D hydrodynamic interactions on confined colloidal suspensions, where only the colloids are restricted to one or two dimensions. In the absence of static interactions among the colloids, i.e., an ideal gas of colloidal particles with a finite hydrodynamic radius, we find a divergent collective diffusion coefficient. The origin of the divergence is traced back to the dimensional mismatch of 3D hydrodynamic interactions and the colloidal particles moving only in 1D or 2D. Our results from theory are confirmed by Stokesian dynamics simulations and supported by light scattering observational data for particles at a fluid interface.
Multiple sulphur and oxygen isotopes reveal microbial sulphur cycling in spring waters in the Lower Engadin, Switzerland
2015-04-29

Highly mineralized springs in the Scuol-Tarasp area of the Lower Engadin and in the Albula Valley near Alvaneu, Switzerland, display distinct differences with respect to the source and fate of their dissolved sulphur species. High sulphate concentrations and positive sulphur (δ(34)S) and oxygen (δ(18)O) isotopic compositions argue for the subsurface dissolution of Mesozoic evaporitic sulphate. In contrast, low sulphate concentrations and less positive or even negative δ(34)S and δ(18)O values indicate a substantial contribution of sulphate sulphur from the oxidation of sulphides in the crystalline basement rocks or the Jurassic sedimentary cover rocks. Furthermore, multiple sulphur (δ(34)S, Δ(33)S) isotopes support the identification of microbial sulphate reduction and sulphide oxidation in the subsurface, the latter is also evident through the presence of thick aggregates of sulphide-oxidizing Thiothrix bacteria.
State-selective all-optical detection of Rydberg atoms
2015-04-29

We present an all-optical protocol for detecting population in a selected Rydberg state of alkali atoms. The detection scheme is based on the interaction of an ensemble of ultracold atoms with two laser pulses: one weak probe pulse which is resonant with the transition between the ground state and the first excited state, and a pulse with high intensity which couples the first excited state to the selected Rydberg state. We show that by monitoring the absorption signal of the probe laser over time, one can deduce the initial population of the Rydberg state. Furthermore, it is shown that - for suitable experimental conditions - the dynamical absorption curve contains information on the initial coherence between the ground state and the selected Rydberg state. We present the results of a proof-of-principle measurement performed on a cold gas of Rb atoms. The method is expected to find application in quantum computing protocols based on Rydberg atoms.
Combined use of SAR and optical data for environmental assessments around refugee camps in semiarid landscapes
2015-04-29

Abstract. Over 15 million people were officially considered as refugees in the year 2012 and another 28 million as internally displaced people (IDPs). Natural disasters, climatic and environmental changes, violent regional conflicts and population growth force people to migrate in all parts of this world. This trend is likely to continue in the near future, as political instabilities increase and land degradation progresses. EO4HumEn aims at developing operational services to support humanitarian operations during crisis situations by means of dedicated geo-spatial information products derived from Earth observation and GIS data. The goal is to develop robust, automated methods of image analysis routines for population estimation, identification of potential groundwater extraction sites and monitoring the environmental impact of refugee/IDP camps. This study investigates the combination of satellite SAR data with optical sensors and elevation information for the assessment of the environmental conditions around refugee camps. In order to estimate their impact on land degradation, land cover classifications are required which target dynamic landscapes. We performed a land use / land cover classification based on a random forest algorithm and 39 input prediction rasters based on Landsat 8 data and additional layers generated from radar texture and elevation information. The overall accuracy was 92.9 %, while optical data had the highest impact on the final classification. By analysing all combinations of the three input datasets we additionally estimated their impact on single classification outcomes and land cover classes.
Overexpression of the glucose transporter 1 in renal mesangial cells protects against cellular stress via Nrf2/NQO1
2015-04-29

Introduction: Diabetic patients have been shown to be susceptible to the formation and accumulation of triose phosphates and the reactive metabolite methylglyoxal (MG), formed by non-enzymatic degradation on these intermediates, suggesting that it is not the condition of hyperglycemia, but how glucose is handled, which underlies the development of diabetic complications. In this study, this was addressed by characterizing rat mesangial cells which stably overexpress the glucose transporter-1 protein, the rate-limiting step for the movement of glucose into the cell. In such cells, glucose uptake and utilization is increased regardless of other regulator factors.
Loss of ALCAM/CD166 partially protects against diabetic nephropathy
2015-04-29

Introduction/Background: Activated leukocyte cell adhesion molecule (ALCAM/CD166) has been shown to function as a pattern recognition receptor, analogue to the receptor of advanced glycation endproducts. In this study role of ALCAM in diabetic nephropathy was investigated in patients with type 2 diabetes, and further investigated in vitro and in vivo using homozygous knock-out mice for ALCAM (ALCAM-/-).
The competing effects of sulfide saturation versus degassing on the behavior of the chalcophile elements during the differentiation of hydrous melts
2015-04-30

Abstract There is a lack of consensus regarding the roles of sulfide saturation versus volatile degassing on the partitioning of Cu and Ag during differentiation and eruption of convergent margin magmas. Because of their oxidized character, volatile‐rich magmas from the Eastern Manus Back‐arc Basin (EMBB) only reach sulfide saturation following magnetite‐driven reduction of the melt: the so‐called “magnetite crisis.” If sulfide saturation typically precedes volatile saturation, the magnetite crisis will limit the proportion of Cu and Ag that can partition from the melt into an exsolving volatile‐rich phase, which may contribute to the sporadic occurrence of magmatic‐hydrothermal ore deposits at convergent margins. However, it is unclear whether the magnetite crisis is a common or rare event during differentiation of volatile‐rich magmas. We report major and trace element data for submarine volcanic glasses from the Tonga arc‐proximal Valu Fa Ridge (VFR; SW Pacific). Cu‐Se‐Ag systematics of samples erupting at the southern VFR suggest magnetite fractionation‐triggered sulfide saturation. The similarity in chalcophile element systematics of the southern VFR and EMBB samples is unlikely to be coincidental, and may indicate that the magnetite crisis is a common event during differentiation of hydrous melts. However, unlike many convergent margin magmas, it is unlikely that the evolving VFR and EMBB were saturated in a S‐bearing volatile phase prior to magnetite fractionation. Hence, the metal‐depleting magnetite crisis may be restricted to back‐arc basin magmas that do not degas volatiles prior to magnetite fractionation and potentially convergent margin magmas fractionating at high pressures in the continental crust.
Tectonic evolution and high-pressure rock exhumation in the Qiangtang terrane, central Tibet
2015-04-30

Abstract. Conflicting interpretations of the &gt; 500 km long, east–west-trending Qiangtang metamorphic belt have led to very different and contradicting models for the Permo–Triassic tectonic evolution of central Tibet. We define two metamorphic events, one that only affected pre-Ordovician basement rocks and one subduction-related Triassic high-pressure metamorphism event. Detailed mapping and structural analysis allowed us to define three main units that were juxtaposed due to collision of the north and south Qiangtang terranes after closure of the Ordovician–Triassic ocean that separated them. The base is formed by the Precambrian–Carboniferous basement, followed by non-metamorphic ophiolitic mélange containing mafic rocks that range in age from the Ordovician to Middle Triassic. The top of the sequence is formed by strongly deformed sedimentary mélange that contains up to &gt; 10 km size rafts of both unmetamorphosed Permian sediments and high-pressure blueschists. We propose that the high-pressure rocks were exhumed from underneath the south Qiangtang terrane in an extensional setting caused by the pull of the northward subducting slab of the Shuanghu–Tethys. High-pressure rocks, sedimentary mélange and margin sediments were thrust on top of the ophiolitic mélange that was scraped off the subducting plate. Both units were subsequently thrust on top of the south Qiantang terrane continental basement. Onset of Late Triassic sedimentation marked the end of the amalgamation of both Qiangtang terranes and the beginning of spreading between Qiantang and north Lhasa to the south, leading to the deposition of thick flysch deposits in the Jurassic.
Control of Morphological Differentiation of Streptomyces coelicolor A3(2) by Phosphorylation of MreC and PBP2
2015-04-30

During morphological differentiation of Streptomyces coelicolor A3(2), the sporogenic aerial hyphae are transformed into a chain of more than fifty spores in a highly coordinated manner. Synthesis of the thickened spore envelope is directed by the Streptomyces spore wall synthesizing complex SSSC which resembles the elongasome of rod-shaped bacteria. The SSSC includes the eukaryotic type serine/threonine protein kinase (eSTPK) PkaI, encoded within a cluster of five independently transcribed eSTPK genes (SCO4775-4779). To understand the role of PkaI in spore wall synthesis, we screened a S. coelicolor genomic library for PkaI interaction partners by bacterial two-hybrid analyses and identified several proteins with a documented role in sporulation. We inactivated pkaI and deleted the complete SCO4775-4779 cluster. Deletion of pkaI alone delayed sporulation and produced some aberrant spores. The five-fold mutant NLΔ4775-4779 had a more severe defect and produced 18% aberrant spores affected in the integrity of the spore envelope. Moreover, overbalancing phosphorylation activity by expressing a second copy of any of these kinases caused a similar defect. Following co-expression of pkaI with either mreC or pbp2 in E. coli, phosphorylation of MreC and PBP2 was demonstrated and multiple phosphosites were identified by LC-MS/MS. Our data suggest that elaborate protein phosphorylation controls activity of the SSSC to ensure proper sporulation by suppressing premature cross-wall synthesis.
CXCR4+granulocytes reflect fungal cystic fibrosis lung disease
2015-04-30

Cystic fibrosis airways are frequently colonised with fungi. However, the interaction of these fungi with immune cells and the clinical relevance in cystic fibrosis lung disease are incompletely understood. We characterised granulocytes in airway fluids and peripheral blood from cystic fibrosis patients with and without fungal colonisation, non-cystic fibrosis disease controls and healthy control subjects cross-sectionally and longitudinally and correlated these findings with lung function parameters. Cystic fibrosis patients with chronic fungal colonisation by Aspergillus fumigatus were characterised by an accumulation of a distinct granulocyte subset, expressing the HIV coreceptor CXCR4. Percentages of airway CXCR4 + granulocytes correlated with lung disease severity in patients with cystic fibrosis. These studies demonstrate that chronic fungal colonisation with A. fumigatus in cystic fibrosis patients is associated with CXCR4 + airway granulocytes, which may serve as a potential biomarker and therapeutic target in fungal cystic fibrosis lung disease.
Swift/BAT measurements of the cyclotron line energy decay in the accreting neutron star Hercules X-1: indication of an evolution of the magnetic field?
2015-04-30

Context: The magnetic field is a crucial ingredient of neutron stars. It governs the physics of accretion and of the resulting high-energy emission in accreting pulsars. Studies of the cyclotron resonant scattering features (CRSFs) seen as absorption lines in the X-ray spectra of the pulsars permit direct measuremets of the field strength. Aims: From an analysis of a number of pointed observations with different instruments, the energy of CRSF, Ecyc, has recently been found to decay in Her X-1, which is one of the best-studied accreting pulsars. We present our analysis of a homogeneous and almost uninterrupted monitoring of the line energy with Swift/BAT. Methods: We analyzed the archival Swift/BAT observations of Her X-1 from 2005 to 2014. The data were used to measure the CRSF energy averaged over several months. Results: The analysis confirms the long-term decay of the line energy. The downward trend is highly significant and consistent with the trend measured with the pointed observations: dEcyc/dt ~-0.3 keV per year. Conclusions: The decay of Ecyc either indicates a local evolution of the magnetic field structure in the polar regions of the neutron star or a geometrical displacement of the line-forming region due to long-term changes in the structure of the X-ray emitting region. The shortness of the observed timescale of the decay, -Ecyc/(dEcyc/dt) ~ 100 yr, suggests that trend reversals and/or jumps of the line energy might be observed in the future.
Simultaneous learning and filtering without delusions: a Bayes-optimal combination of Predictive Inference and Adaptive Filtering
2015-04-30

Predictive coding appears to be one of the fundamental working principles of brain processing. Amongst other aspects, brains often predict the sensory consequences of their own actions. Predictive coding resembles Kalman filtering, where incoming sensory information is filtered to produce prediction errors for subsequent adaptation and learning. However, to generate prediction errors given motor commands, a suitable temporal forward model is required to generate predictions. While in engineering applications, it is usually assumed that this forward model is known, the brain has to learn it. When filtering sensory input and learning from the residual signal in parallel, a fundamental problem arises: the system can enter a delusional loop when filtering the sensory information using an overly trusted forward model. In this case, learning stalls before accurate convergence because uncertainty about the forward model is not properly accommodated. We present a Bayes-optimal solution to this generic and pernicious problem for the case of linear forward models, which we call Predictive Inference and Adaptive Filtering (PIAF). PIAF filters incoming sensory information and learns the forward model simultaneously. We show that PIAF is formally related to Kalman filtering and to the Recursive Least Squares linear approximation method, but combines these procedures in a Bayes optimal fashion. Numerical evaluations confirm that the delusional loop is precluded and that the learning of the forward model is more than 10-times faster when compared to a naive combination of Kalman filtering and Recursive Least Squares.
Spatial displacement of numbers on a vertical number line in spatial neglect
2015-04-30

Previous studies that investigated the association of numbers and space in humans came to contradictory conclusions about the spatial character of the mental number magnitude representation and about how it may be influenced by unilateral spatial neglect. The present study aimed to disentangle the debated influence of perceptual vs. representational aspects via explicit mapping of numbers onto space by applying the number line estimation paradigm with vertical orientation of stimulus lines. Thirty-five acute right-brain damaged stroke patients (6 with neglect) were asked to place two-digit numbers on vertically oriented lines with 0 marked at the bottom and 100 at the top. In contrast to the expected, nearly linear mapping in the control patient group, patients with spatial neglect overestimated the position of numbers in the lower middle range. The results corroborate spatial characteristics of the number magnitude representation. In neglect patients, this representation seems to be biased towards the ipsilesional side, independent of the physical orientation of the task stimuli.
SIMULTANEOUS FITS IN ISIS ON THE EXAMPLE OF GRO J1008–57
2015-04-30

&lt;p&gt;Parallel computing and steadily increasing computation speed have led to a new tool for analyzing multiple datasets and datatypes: fitting several datasets simultaneously. With this technique, physically connected parameters of individual data can be treated as a single parameter by implementing this connection directly into the fit. We discuss the terminology, implementation, and possible issues of simultaneous fits based on the Interactive Spectral Interpretation System (ISIS) X-ray data analysis tool. While all data modeling tools in X-ray astronomy in principle allow data to be fitted individually from multiple data sets, the syntax used in these tools is not often well suited for this task. Applying simultaneous fits to the transient X-ray binary GRO J1008–57, we find that the spectral shape is only dependent on X-ray flux. We determine time independent parameters e.g., the folding energy E&lt;sub&gt;fold&lt;/sub&gt;, with unprecedented precision.&lt;/p&gt;
Assessment of murine brain tissue shrinkage caused by different histological fixatives using magnetic resonance and computed tomography imaging.
2015-05-01

Especially for neuroscience and the development of new biomarkers, a direct correlation between in vivo imaging and histology is essential. However, this comparison is hampered by deformation and shrinkage of tissue samples caused by fixation, dehydration and paraffin embedding. We used magnetic resonance (MR) imaging and computed tomography (CT) imaging to analyze the degree of shrinkage on murine brains for various fixatives. After in vivo imaging using 7 T MRI, animals were sacrificed and the brains were dissected and immediately placed in different fixatives, respectively: zinc-based fixative, neutral buffered formalin (NBF), paraformaldehyde (PFA), Bouin-Holland fixative and paraformaldehyde-lysine-periodate (PLP). The degree of shrinkage based on mouse brain volumes, radiodensity in Hounsfield units (HU), as well as non-linear deformations were obtained. The highest degree of shrinkage was observed for PLP (68.1%, P < 0.001), followed by PFA (60.2%, P<0.001) and NBF (58.6%, P<0.001). The zinc-based fixative revealed a low shrinkage with only 33.5% (P<0.001). Compared to NBF, the zinc-based fixative shows a slightly higher degree of deformations, but is still more homogenous than PFA. Tissue shrinkage can be monitored non-invasively with CT and MR. Zinc-based fixative causes the smallest degree of brain shrinkage and only small deformations and is therefore recommended for in vivo ex vivo comparison studies.
How to rapidly construct a spatial–numerical representation in preliterate children (at least temporarily)
2015-05-01

Abstract Spatial processing of numbers has emerged as one of the basic properties of humans’ mathematical thinking. However, how and when number–space relations develop is a highly contested issue. One dominant view has been that a link between numbers and left/right spatial directions is constructed based on directional experience associated with reading and writing. However, some early forms of a number–space link have been observed in preschool children who cannot yet read and write. As literacy experience is evidently not necessary for number–space effects, we are searching for other potential sources of this association. Here we propose and test a hypothesis that the number–space link can be quickly constructed in preschool children's cognition on the basis of spatially oriented visuo‐motor activities. We trained 3‐ and 4‐year‐old children with a non‐numerical spatial movement task (left‐to‐right or right‐to‐left), where via touch screen children had to move a frog across a pond. After the training, children had to perform a numerosity comparison task. After left‐to‐right training, we observed a SNARC ‐like effect (reactions to smaller numbers were faster on the left side, and reactions to larger numbers on the right side), and after right‐to‐left training a reverse effect. These results are the first to show a causal link between visuo‐motor activities and number–space associations in children before they learn to read and write. We argue that simple activities, such as manual games, dominant in a given society, might shape number–space associations in children in a way similar to lifelong reading training.