julilili42/papers huggingface dataset:
Screen space spherical harmonics occlusion (S 3 HO) sampling
2011-08-07

One objective of global illumination (GI) models is to solve the lighting integral of the upper hemisphere at a surface point. One particular effect of GI that has become very popular in the past years is Ambient Occlusion (AO), where, independently of the lighting, a coverage factor that indicates the amount of occlusion induced by its local neighboring geometry is calculated for every surface point. Screen Space Ambient Occlusion (SSAO) algorithms allow for the approximation of this occlusion factor in real time. Ritschel et al. [2009] proposed Screen Space Directional Occlusion (SSDO), combining the calculation of occlusion and lighting by simultaneously accumulating the light of unoccluded directions when sampling the occlusion. Contrary to AO this results in colored shadows simulating directional lighting effects. Green [2003] outlined techniques based on Spherical Harmonics (SH) that approximate global lighting models with the basic principle of representing both, the incoming radiance field and the occlusion, as functions defined on the sphere that can be efficiently represented in the spherical Fourier domain. Calculating the spherical occlusion function, however, remains computationally expensive since ray tracing methods have to be applied.
Multispan mitochondrial outer membrane protein Ugo1 follows a unique Mim1-dependent import pathway
2011-08-08

The mitochondrial outer membrane (MOM) harbors several multispan proteins that execute various functions. Despite their importance, the mechanisms by which these proteins are recognized and inserted into the outer membrane remain largely unclear. In this paper, we address this issue using yeast mitochondria and the multispan protein Ugo1. Using a specific insertion assay and analysis by native gel electrophoresis, we show that the import receptor Tom70, but not its partner Tom20, is involved in the initial recognition of the Ugo1 precursor. Surprisingly, the import pore formed by the translocase of the outer membrane complex appears not to be required for the insertion process. Conversely, the multifunctional outer membrane protein mitochondrial import 1 (Mim1) plays a central role in mediating the insertion of Ugo1. Collectively, these results suggest that Ugo1 is inserted into the MOM by a novel pathway in which Tom70 and Mim1 contribute to the efficiency and selectivity of the process.
FraC/FraD‐dependent intercellular molecular exchange in the filaments of a heterocyst‐forming cyanobacterium, Anabaena sp.
2011-08-08

Summary The filamentous, heterocyst‐forming cyanobacteria are multicellular organisms in which two different cell types, the CO 2 ‐fixing vegetative cells and the N 2 ‐fixing heterocysts, exchange nutrients and regulators. In Anabaena sp. strain PCC 7120, inactivation of sepJ or genes in the fraC operon ( fraC , fraD and fraE ) produce filament fragmentation. SepJ, FraC and FraD are cytoplasmic membrane proteins located in the filament's intercellular septa that are needed for intercellular exchange of the fluorescent tracer calcein (622 Da). Transmission electron microscopy showed an alteration in the heterocyst cytoplasmic membrane at the vegetative cell‐heterocyst septa in Δ fraC and Δ fraD mutants. Immunogold labelling of FraD confirmed its localization in the intercellular septa and clearly showed the presence of part of the protein between the cytoplasmic membranes of the adjacent cells. This localization seemed to be affected in the Δ fraC mutant but was not impaired in a Δ sepJ mutant. Intercellular transfer of a smaller fluorescent tracer, 5‐carboxyfluorescein (374 Da), was largely impaired in Δ fraC , Δ fraD and double Δ fraC‐ Δ fraD mutants, but much less in the Δ sepJ mutant. These results show the existence in the Anabaena filaments of a FraC/FraD‐dependent intercellular molecular exchange that does not require SepJ.
A Hypothesis about the Biological Basis of Expert Intuition
2011-08-08

It is well established that intuition plays an important role in experts’ decision making and thinking generally. However, the theories that have been developed at the cognitive level have limits in their explanatory power and lack detailed explanation of the underlying biological mechanisms. In this paper, we bridge this gap by proposing that Hebb's (1949) concept of cell assembly is the biological realization of Simon's (1974) concept of chunking. This view provides mechanisms at the biological level that are consistent with both biological and psychological findings. To further address the limits of previous theories, we introduce emotions as a component of intuition by showing how they modulate the perception-memory interaction. The idea that intuition lies at the crossroads between perception, knowledge, and emotional modulation sheds new light on the phenomena of expertise and intuition.
Stimulation of erythrocyte phospholipid scrambling by enniatin A
2011-08-08

Abstract Scope : Enniatin A, a peptide antibiotic and common food contaminant, triggers mitochondrial dysfunction and apoptosis. Even though lacking mitochondria, erythrocytes may similarly undergo suicidal cell death or eryptosis. Eryptosis is characterized by cell shrinkage and cell membrane phospholipid scrambling. Triggers of phospholipid scrambling include energy depletion and increase in cytosolic Ca 2+ activity ([Ca 2+ ] i ). The present study explored whether enniatin A triggers phospholipid scrambling. Methods and results : Phospholipid scrambling was estimated from annexin‐V‐binding, cell volume from forward scatter (FSC), [Ca 2+ ] i from Fluo3‐fluorescence, cytosolic ATP‐concentration ([ATP] i ) using a luciferase assay and hemolysis from hemoglobin release. Exposure of erythrocytes for 48 h to enniatin A (≥2.5 μM) significantly increased [Ca 2+ ] i , decreased [ATP] i , decreased FSC, triggered annexin‐V‐binding and elicited hemolysis. Annexin‐V‐binding affected 25%, and hemolysis 2% of treated erythrocytes. Decreased [ATP] i by glucose depletion for 48 h was similarly followed by increased [Ca 2+ ] i , decreased FSC and annexin‐V‐binding. Enniatin A augmented the effect on [Ca 2+ ] i and annexin‐V‐binding, but not on FSC. Annexin‐V‐binding was blunted by Ca 2+ removal, by the cation channel inhibitor amiloride (1 mM), by the protein kinase C inhibitor staurosporine (500 nM) but not by the pancaspase inhibitor zVAD (10 μM). Conclusion : The food contaminant enniatin A triggers ATP depletion and increases cytosolic Ca 2+ activity, effects resulting in suicidal erythrocyte death.
Nanoscale Probing of Dielectric Interfaces with Single-Molecule Excitation Patterns and Radially Polarized Illumination
2011-08-08

We present new results on the theoretical and experimental study of the excitation patterns acquired upon scanning a single molecule through the focal region of a radially polarized laser beam when the emitter is located at a glass–air interface and in bulk glass. Our calculations show that the presence of a dielectric interface, which coincides with the focal plane of a radially polarized laser beam, strongly changes the field intensity distribution within the focus, which results in the modification of the single molecule excitation pattern obtained upon scanning a molecule through the focal region. By changing the dielectric properties of the surrounding media in situ we show experimentally that the same individual molecule possessing the same orientation with respect to the laser beam axis exhibits different shapes of excitation patterns, depending on whether it is located on the dielectric interface or in medium with constant refractive index.
6-(4-Chlorophenyl)-7-phenyl-2,3-dihydro-1H-pyrrolizine-5-carbaldehyde
2011-08-10

The 4-meth-oxy-phenyl residue in the title compound, C(21)H(19)NO(2), is oriented at a dihedral angle of 54.6 (5)° with respect to the phenyl ring and at a dihedral angle of 52.5 (8)° with respect to the pyrrole ring of the pyrrolizine system. The phenyl ring is oriented at a dihedral angle of 36.2 (5)° with respect to the pyrrole ring. The meth-oxy group makes a C-C-O-C torsion angle of 3.8 (9)° with the attached benzene ring.
Paroxysmal choreoathetosis/spasticity (DYT9) is caused by a GLUT1 defect
2011-08-11

This study shows that DYT9 and DYT18 are allelic disorders and enlarges the spectrum of GLUT1 phenotypes, now also including slowly progressive spastic paraparesis combined with PED. SLC2A1 mutations were excluded as a cause of HSP without PED in our cohort.
Discovery of the source HESS J1356-645 associated with the young and energetic PSR J1357-6429
2011-08-11

Context. Several newly discovered very-high-energy (VHE; E &gt; 100 GeV) γ-ray sources in the Galaxy are thought to be associated with energetic pulsars. Among them, middle-aged (≳ 104 yr) systems exhibit large centre-filled VHE nebulae, offset from the pulsar position, which result from the complex relationship between the pulsar wind and the surrounding medium, and reflect the past evolution of the pulsar.&#13;\\n&#13;\\nAims. Imaging Atmospheric Cherenkov Telescopes (IACTs) have been successful in revealing extended emission from these sources in the VHE regime. Together with radio and X-ray observations, this observational window allows one to probe the energetics and magnetic field inside these large-scale nebulae.&#13;\\n&#13;\\nMethods. H.E.S.S., with its large field of view, angular resolution of ≲0.1° and unprecedented sensitivity, has been used to discover a large population of such VHE sources. In this paper, the H.E.S.S. data from the continuation of the Galactic Plane Survey (− 80° &lt; l &lt; 60°, |b| &lt; 3°), together with the existing multi-wavelength observations, are used.&#13;\\n&#13;\\nResults. A new VHE γ-ray source was discovered at RA (J2000) = 13h56m00s, Dec (J2000) = −64°30′00′′ with a 2′ statistical error in each coordinate, namely HESS J1356−645. The source is extended, with an intrinsic Gaussian width of (0.20 ± 0.02)°. Its integrated energy flux between 1 and 10 TeV of 8 × 10-12 erg cm-2 s-1 represents ~11% of the Crab Nebula flux in the same energy band. The energy spectrum between 1 and 20 TeV is well described by a power law dN/dE ∝ E−Γ with photon index Γ = 2.2 ± 0.2stat ± 0.2sys. The inspection of archival radio images at three frequencies and the analysis of X-ray data from ROSAT/PSPC and XMM-Newton/MOS reveal the presence of faint non-thermal diffuse emission coincident with HESS J1356−645.&#13;\\n&#13;\\nConclusions. HESS J1356−645 is most likely associated with the young and energetic pulsar PSR J1357−6429 (d = 2.4 kpc, τc = 7.3 kyr and Ė = 3.1 × 1036 erg s-1), located at a projected distance of ~5 pc from the centroid of the VHE emission. HESS J1356−645 and its radio and X-ray counterparts would thus represent the nebula resulting from the past history of the PSR J1357−6429 wind. In a simple one-zone model,
Emergency obstetric care availability: a critical assessment of the current indicator
2011-08-11

Abstract Monitoring progress in reducing maternal and perinatal mortality requires suitable indicators. The density of emergency obstetric care (EmOC) facilities has been proposed as a potentially useful indicator, but different UN documents make inconsistent recommendations, and its current formulation is not associated with maternal mortality. We compiled recently published indicator benchmarks and distinguished three sources of inconsistency: (i) use of different denominator metrics (per birth and per population), (ii) different assumptions on need for EmOC and for EmOC facilities and (iii) failure to specify facility capacity (birth load). The UN guidelines and handbook require fewer EmOC facilities than the World Health Report 2005 and do not specify capacity for deliveries or staffing levels. We recommend (i) always using births as the denominator for EmOC facility density, (ii) clearly stating assumptions on the proportion of deliveries needing basic and comprehensive emergency obstetric care and the desired proportion of deliveries in EmOC facilities and (iii) specifying facility capacity and staffing and adapting benchmarks for settings with different population density to ensure geographical accessibility.
Effect of leukotriene inhibitors on evolution of experimental brain contusions
2011-08-11

C. Voigt, C. K. Donat, W. Hartig, A. Förschler, M. Skardelly, D. Stichtenoth, T. Arendt, J. Meixensberger and M. U. Schuhmann (2012) Neuropathology and Applied Neurobiology 38, 354–366 Effect of leukotriene inhibitors on evolution of experimental brain contusions Aims: Leukotriene levels increase in cerebrospinal fluid (CSF) following controlled cortical impact (CCI) injury in rats. We investigated the impact of two different leukotriene inhibitors in the CCI model on CSF leukotriene levels, brain water content (BWC), brain swelling (BS) contusion size and cellular response. Methods: 134 male Sprague Dawley rats were investigated at 4, 24 and 72 h after CCI for CSF leukotriene levels and BWC/BS, lesion size in T2‐weighted magnetic resonance imaging and immunohistochemistry. Animals received vehicle, MK‐886, an inhibitor of 5‐lipoxygenase activating protein, or Boscari ® , a mixture of boswellic acids, acting as competitive nonredox 5‐lipoxygenase inhibitors before trauma and then every 8 h until sacrifice. Results: The intracranial pressure (ICP) was unaffected by treatment. Boscari treatment reduced CSF leukotriene C4 increase by −45% at 4 h ( P &lt; 0.03) and increase of BWC and BS by 49% ( P &lt; 0.05) and −58% at 24 h. Treatment with both substances showed a reduction of lesion volume at 72 h by −21% ( P &lt; 0.01) in T 2 ‐weighted magnetic resonance imaging, which was reflected in a smaller lesion area determined from a NeuN labelled section (−17% to −20%, P &lt; 0.05). Triple immunofluorescence and Fluoro‐Jade B staining showed rarefaction of neurones, glia and vasculature in the contusion core, whereas in the pericontusional zone astro‐ and microglia were upregulated in the presence of dying neurones. Treatment resulted in an improved survival of NeuN labelled neurones in the pericontusional cortex (+15% to +20%, P &lt; 0.05). Conclusions: Leukotriene inhibition should be further investigated as therapeutic option to counteract secondary growth of traumatic brain contusions and to possibly improve pericontusional neuronal survival.
ChemInform Abstract: Refined Crystal Structure and Idealized Structure of Mixed‐Valent Eu4F5(CN2)2: Transition Possible.
2011-08-11

Abstract The title compound is prepared by solid state reaction of EuF 3 , EuF 2+x , and Li 2 (CN 2 ) at 700 °C and characterized by single crystal XRD, 151 Eu Moessbauer spectroscopy, and magnetic measurements.
Evidence for the localization of the Arabidopsis cytokinin receptors AHK3 and AHK4 in the endoplasmic reticulum
2011-08-12

Cytokinins are hormones that are involved in various processes of plant growth and development. The model of cytokinin signalling starts with hormone perception through membrane-localized histidine kinase receptors. Although the biochemical properties and functions of these receptors have been extensively studied, there is no solid proof of their subcellular localization. Here, cell biological and biochemical evidence for the localization of functional fluorophor-tagged fusions of Arabidopsis histidine kinase 3 (AHK3) and 4 (AHK4), members of the cytokinin receptor family, in the endoplasmic reticulum (ER) is provided. Furthermore, membrane-bound AHK3 interacts with AHK4 in vivo. The ER localization and putative function of cytokinin receptors from the ER have major impacts on the concept of cytokinin perception and signalling, and hormonal cross-talk in plants.
Arthrofibrosis after TKA - Influence factors on the absolute flexion and gain in flexion after manipulation under anaesthesia
2011-08-12

Abstract Background Stiffness with decreased range of motion (ROM) has been described as a frustrating complication after TKA. If all methods of physiotherapeutic treatment have been exhausted trying to develop ROM, manipulation under anaesthesia (MUA) can be discussed. The aim of the present study was to show the effect of MUA and to determine the influence of BMI, number of previous surgical procedures, pre-MUA ROM and timing of MUA for the results after MUA in regard to absolute flexion and gain in flexion. Methods 858 patients underwent TKA at our institution between 2004 and 2009. 39 of these patients underwent MUA because of postoperative knee stiffness. The data were retrospective analysed for the influence of BMI, pre-MUA flexion (&lt;/≥ 70°), timing of MUA (&gt;/≤ 30 days after TKA) and number of previous surgery on the results after MUA (absolute Flexion/gain in flexion). Results The prevalence for stiffness after TKA was 4.54%. There was a statistically significant improvement in flexion not only directly after MUA but also 6 weeks after MUA. Patients with two or more previous operations before TKA showed statistically significant worse results six weeks after MUA in absolute flexion and gain in flexion (p = 0.039) than patients with one or two previous operations. No statistical significance in absolute flexion (p = 0.655) and gain in flexion (p = 0.328) after MUA between "early" and "late" was detected. The stiffer knees with a flexion below 70° showed significantly worse results (p = 0.044) in absolute flexion six weeks after MUA, but they also had statistical statistically better results with regard to gain in flexion (p ≤ 0.001). Conclusion MUA is a good instrument for improving ROM after TKA. The time between TKA and MUA seems less important, so different types of physiotherapeutic treatment could be tried before the procedure is started. MUA in patients with many previous operations and a flexion of less than 70° before MUA is not as effective as in other patients, but they also benefit from MUA.
Functional anatomy of the Arabidopsis cytokinesis‐specific syntaxin KNOLLE
2011-08-12

Summary In plant cytokinesis, Golgi/ trans ‐Golgi network‐derived vesicles are targeted to the plane of cell division where they fuse with one another to form the partitioning membrane (cell plate). This membrane fusion requires a specialised syntaxin (Qa‐SNARE), named KNOLLE in Arabidopsis. KNOLLE is only made during the M‐phase of the cell cycle, targeted to the plane of cell division and degraded in the vacuole at the end of cytokinesis. To identify the parts of KNOLLE required for proper targeting and function in membrane fusion, we generated chimeric syntaxins comprising complementary fragments from KNOLLE and MVB‐localized PEP12 (SYP21). Surprisingly, targeting of the chimeric protein was not specified by the C‐terminal membrane anchor. Rather the N‐terminal region including helix Ha and the adjacent linker to helix Hb appeared to played a critical role. However, deletion of this N‐terminal fragment from KNOLLE (KN Δ1–82 ) had the same effect as its presence in the chimeric protein (KN 1–82 ‐PEP12 64–279 ), suggesting that targeting to the plane of cell division occurs by default, i.e. when no sorting signal would target the syntaxin to a specific endomembrane compartment. Once the full‐length syntaxin accumulated at the plane of division, phenotypic rescue of the knolle mutant only required the SNARE domain plus the adjacent linker connecting helix Hc to the SNARE domain from KNOLLE. Our results suggest that targeting of syntaxin to the plane of cell division occurs without active sorting, whereas syntaxin‐mediated membrane fusion requires sequence‐specific features.
LOCAS – A Low Coverage Assembly Tool for Resequencing Projects
2011-08-15

LOCAS produces excellent results for homology-guided assembly of eukaryotic genomes with short reads and low sequencing depth, and therefore appears to be the assembly tool of choice for the detection of novel sequence variations in this scenario.
Towards improved instrumentation for assessing river-groundwater interactions in a restored river corridor
2011-08-16

Abstract. River restoration projects have been launched over the last two decades to improve the ecological status and water quality of regulated rivers. As most restored rivers are not monitored at all, it is difficult to predict consequences of restoration projects or analyze why restorations fail or are successful. It is thus necessary to implement efficient field assessment strategies, for example by employing sensor networks that continuously measure physical parameters at high spatial and temporal resolution. This paper focuses on the design and implementation of an instrumentation strategy for monitoring changes in bank filtration, hydrological connectivity, groundwater travel time and quality due to river restoration. We specifically designed and instrumented a network of monitoring wells at the Thur River (NE Switzerland), which is partly restored and has been mainly channelized for more than 100 years. Our results show that bank filtration – especially in a restored section with alternating riverbed morphology – is variable in time and space. Consequently, our monitoring network has been adapted in response to that variability. Although not available at our test site, we consider long-term measurements – ideally initiated before and continued after restoration – as a fundamental step towards predicting consequences of river restoration for groundwater quality. As a result, process-based models could be adapted and evaluated using these types of high-resolution data sets.
Effect of geographical range size on plant functional traits and the relationships between plant, soil and climate in Chinese grasslands
2011-08-16

ABSTRACT Aim Our aim was to address the potential effect of the geographical range size of species on the relationships between plant traits, soil and climate in Chinese grasslands. Previous analyses tended to examine plant–environment relationships across many species while ignoring that species with different range sizes may respond differently to the environment. Here we hypothesized that leaf traits of narrow‐ranging species would be more strongly correlated with soil and climatic variables than those of wide‐ranging species. Location Chinese grasslands. Methods Data on leaf traits, including nitrogen and phosphorus concentrations, carbon/nitrogen ratio, nitrogen/phosphorus ratio and specific leaf area, as well as species range sizes for 208 species distributed across 178 sites in Chinese grasslands were collected. Soil and climate information for each study site was also gathered. The effects of range size on leaf traits were tested using one‐way ANOVA. Correlations between leaf traits, soil and climate were calculated for all species pooled together and for species partitioned into range size quartiles, from the first (narrowest‐ ranging 25%) to the fourth (widest‐ranging 25%). Results Narrow‐ranging species tended to occur at high altitude with lower temperature but higher soil nutrient concentrations compared with wide‐ranging species. No direct link between leaf traits and species range sizes was detected. However, patterns of leaf–soil nutrient relationships changed significantly across levels of range size. Narrow‐ranging species tended to be more sensitive to variation in soil nutrient availability than wide‐ranging species, resulting in a shift from a positive leaf–soil nutrient relationship for narrow‐ranging plants to no relationship for wide‐ranging plants. Species responses to climatic variables were unrelated to their range sizes. Main conclusions The close relationship between leaf and soil nutrients indicates a specialization of narrow‐ranging species to particular habitats whereas wide‐ranging species may be able to better withstand changes in environment such as soil fertility over a large area.