julilili42/papers huggingface dataset:
Penetration of Light into Multiple Scattering Media: Model Calculations and Reflectance Experiments. Part I: The Axial Transfer
2012-07-25

The article presents two general equations of radiation penetration into layers of diffuse reflectors. One of the equations describes the depth origins of reflection, the other the depth profiles of absorption. The equations are evaluated within the theory of radiative transfer applying various degrees of analytical approximations and Monte Carlo simulations. The data are presented for different scattering and absorption coefficients, arbitrary layer thicknesses, collimated and diffused irradiation, and anisotropic forward scattering. The calculated mean depths of reflection are always lower than the mean depths of absorption. For nearly non-absorbing layers, the mean depths of absorption are about one third of the physical layer thickness. In contrast, penetration saturates for strong absorbers at very low depth levels. From the simulated data, methods are derived for the determination of the penetration depth from reflectance and transmittance data of thin layers or from radially diffused reflectance profiles upon spot irradiation. The methods are experimentally verified for a series of metal oxide powders with particle sizes ranging from much smaller to much larger than the wavelength of irradiation and for microcrystalline cellulose stained with different concentrations of an organic dye.
L-2 hydroxyglutaric aciduria as a rare cause of leukencephalopathy in adults
2012-07-25

Paraoxonase 3 (PON3) is an oncogene in cancer, however, little is known about the mechanisms and roles of PON3 in oral squamous cell carcinoma (OSCC), which is the aim of our study. We found that the expression of PON3 was up-regulated in OSCC samples and cell lines. PON3 was associated with accelerating cell proliferation, cell cycle, migration and invasion in OSCC cells. Further research showed that PON3 was regulated by PI3K/Akt pathway. We also found that AP-1 was an important transcriptional factor regulating PON3 expression in OSCC. The study elucidates that PI3K/Akt pathway up-regulated the expression of PON3 in OSCC by AP-1.
The Uncoordinated-5 Homolog B Receptor Affects Hepatic Ischemia Reperfusion Injury
2012-07-25

Recent evidence has demonstrated additional roles for the neuronal guidance protein receptor UNC5B outside the nervous system. Given the fact that ischemia reperfusion injury (IRI) of the liver is a common source of liver dysfunction and the role of UNC5B during an acute inflammatory response we investigated the role of UNC5B on acute hepatic IRI. We report here that UNC5B(+/-) mice display reduced hepatic IRI and neutrophil (PMN) infiltration compared to WT controls. This correlated with serum levels of lactate dehydrogenase (LDH), aspartate- (AST) and alanine- (ALT) aminotransferase, the presence of PMN within ischemic hepatic tissue, and serum levels of inflammatory cytokines. Moreover, injection of an anti-UNC5B antibody resulted in a significant reduction of hepatic IR injury. This was associated with reduced parameters of liver injury (LDH, ALT, AST) and accumulation of PMN within the injured hepatic tissue. In conclusion our studies demonstrate a significant role for UNC5B in the development of hepatic IRI and identified UNC5B as a potential drug target to prevent liver dysfunction in the future.
Self‐assembly and structure formation in liquid crystalline phthalocyanine thin films studied by Raman spectroscopy and AFM
2012-07-25

This work presents an investigation of films prepared by doctor blade casting, the formation of self‐assembled microstructures of a liquid crystalline phthalocyanine with highly oriented molecules. Raman Spectroscopy in combination with atomic force microscopy is applied to study the structures within the films. By keeping the substrate at room temperature or at 353 K during coating, different geometric structures namely rods and islands form. Rod‐like structures are growing in coating direction, whereas directional growth of the islands is not observed. The distribution of the rod lengths varies widely, whereas the width appears more uniform. Annealing of the samples shows a different behavior of the two textures. Islands tend to melt, and rods smooth their structural form, which is extracted from Raman imaging in combination with atomic force microscopy. Additionally, Raman imaging gives insight into laterally different relative crystallinity. These observations are discussed in the context of the molecular orientation as probed by polarized Raman spectroscopy. These polarized Raman spectra indicate azimuthal alignment of the molecules within the rods (edge on alignment). This alignment occurs along and also perpendicular to the growth direction. In contrast to the alignment in the rods, the molecules inside the islands occurring at higher temperature do not show preferential molecular orientation. After annealing, no preferential molecular orientation is observed in rods because of the loss of anisotropy, too. Copyright © 2012 John Wiley &amp; Sons, Ltd.
Structures of Merkel Cell Polyomavirus VP1 Complexes Define a Sialic Acid Binding Site Required for Infection
2012-07-26

The recently discovered human Merkel cell polyomavirus (MCPyV or MCV) causes the aggressive Merkel cell carcinoma (MCC) in the skin of immunocompromised individuals. Conflicting reports suggest that cellular glycans containing sialic acid (Neu5Ac) may play a role in MCPyV infectious entry. To address this question, we solved X-ray structures of the MCPyV major capsid protein VP1 both alone and in complex with several sialylated oligosaccharides. A shallow binding site on the apical surface of the VP1 capsomer recognizes the disaccharide Neu5Ac-α2,3-Gal through a complex network of interactions. MCPyV engages Neu5Ac in an orientation and with contacts that differ markedly from those observed in other polyomavirus complexes with sialylated receptors. Mutations in the Neu5Ac binding site abolish MCPyV infection, highlighting the relevance of the Neu5Ac interaction for MCPyV entry. Our study thus provides a powerful platform for the development of MCPyV-specific vaccines and antivirals. Interestingly, engagement of sialic acid does not interfere with initial attachment of MCPyV to cells, consistent with a previous proposal that attachment is mediated by a class of non-sialylated carbohydrates called glycosaminoglycans. Our results therefore suggest a model in which sialylated glycans serve as secondary, post-attachment co-receptors during MCPyV infectious entry. Since cell-surface glycans typically serve as primary attachment receptors for many viruses, we identify here a new role for glycans in mediating, and perhaps even modulating, post-attachment entry processes.
FOXO3 Is a Glucocorticoid Receptor Target and Regulates LKB1 and Its Own Expression Based on Cellular AMP Levels via a Positive Autoregulatory Loop
2012-07-27

FOXO3 is a transcription factor involved in the regulation of multiple physiological processes including cell cycle arrest, apoptosis, oxidative stress-response and energy metabolism. Although much is known about its post-translational modification, the transcriptional regulation of FOXO3, as well as the cross-talk between transcription and post-translational events, is still poorly understood. In the present study, we show that FOXO3 is an immediate early glucocorticoid receptor (GR) target, whose transcription is even further enhanced by conditions that mimic metabolic stress. Induction of FOXO3 transcription by GR-binding steroids was reversed by concomitant treatment with the GR antagonist RU-486, but further enhanced by stimuli that activate the AMP-activated protein kinase (AMPK). Analysis of genomic DNA and chromatin immunoprecipitation, as well as luciferase reporter assays, revealed two functional glucocorticoid responsive elements within the FOXO3 promoter. Furthermore, we provide functional evidence for a phosphorylation switch that explains how glucocorticoids induce transcriptional activation of the gene but subsequently inactivate the corresponding protein by site-specific phosphorylation. Only when AMPK is stimulated, pre-existing FOXO3 becomes reverted toward an active form. Energy deprived conditions thus activate FOXO3 on two different levels, namely transcriptional and post-translational. In that way, FOXO3 acts as a metabolic stress sensor that coordinates expression of LKB1, the master upstream kinase involved in metabolic sensing, depending on the energy status of the cell. Additionally, we show that FOXO3 binds and activates its own promoter via a positive autoregulatory feedback loop. In conclusion, our data explain how catabolic glucocorticoid hormones and high intracellular AMP levels cooperate in inducing FOXO3 transcription and in activating the corresponding protein.
The Two-Component Signal Transduction System ArlRS Regulates Staphylococcus epidermidis Biofilm Formation in an ica-Dependent Manner
2012-07-27

Due to its ability to form biofilms on medical devices, Staphylococcus epidermidis has emerged as a major pathogen of nosocomial infections. In this study, we investigated the role of the two-component signal transduction system ArlRS in regulating S. epidermidis biofilm formation. An ArlRS-deficient mutant, WW06, was constructed using S. epidermidis strain 1457 as a parental strain. Although the growth curve of WW06 was similar to that of SE1457, the mutant strain was unable to form biofilms in vitro. In a rabbit subcutaneous infection model, sterile disks made of polymeric materials were implanted subcutaneously followed with inoculation of WW06 or SE1457. The viable bacteria cells of WW06 recovered from biofilms on the embedded disks were much lower than that of SE1457. Complementation of arlRS genes expression from plasmid in WW06 restored biofilm-forming phenotype both in vivo and in vitro. WW06 maintained the ability to undergo initial attachment. Transcription levels of several genes involved in biofilm formation, including icaADBC, sigB, and sarA, were decreased in WW06, compared to SE1457; and icaR expression was increased in WW06, detected by real-time reverse-transcription PCR. The biofilm-forming phenotype was restored by overexpressing icaADBC in WW06 but not by overexpressing sigB, indicating that ArlRS regulates biofilm formation through the regulation of icaADBC. Gel shift assay showed that ArlR can bind to the promoter region of the ica operon. In conclusion, ArlRS regulates S. epidermidis biofilm formation in an ica-dependent manner, distinct from its role in S. aureus.
Superficial Wound Swabbing
2012-07-27

OBJECTIVE In diabetic foot ulcers, wound fluid inflammatory mediators have previously been proposed as surrogate markers for nonhealing. However, currently available wound fluid sampling techniques are not suitable for clinical practice due to low levels of exudate and a high logistical effort. The aim of this investigation was to assess 1) the technique of superficial wound swabbing for harvesting wound fluid; and 2) the quality of the collected fluid for immunoassay analysis of inflammatory mediators. RESEARCH DESIGN AND METHODS Both nylon-flocked swabs and film dressings were used to collect wound fluid from foot ulcers of diabetic patients. In randomly selected patients, levels of wound fluid inflammatory mediators and matrix metalloproteases were determined using multiplexed bead-based sandwich immunoassays with respect to both sampling methods. Wound fluid spike-in experiments were performed to evaluate the impact of different sample processing protocols on subsequent immunoassay analysis. RESULTS Using the swabbing technique, a median amount of 40 μL (2–120 μL) wound exudate was collected, which allowed the measurement of several multiplex panels. Comparing both sampling methods, a similar qualitative protein recovery was observed with a trend to analyte enrichment by swabbing. Sample processing using swabs did not affect analyte recovery, with the exception of interleukin (IL)-8, thymus and activation-regulated chemokine, IL-17A, interferon-γ–induced protein 10, and IL-4. CONCLUSIONS The quality of wound fluid collected by superficial swabbing is not inferior to the current standard technique. Combined with subsequent bead-based sandwich immunoassay analysis, this new method offers a noninvasive technique, suitable for daily clinical routines, for assessment of inflammatory activity in diabetic foot ulcers.
Portuguese living standards, 1720–1980, in European comparison: heights, income, and human capital1
2012-07-27

When and why did the Portuguese become the shortest Europeans? In order to find the answer to this question, we trace the trend in Portuguese living standards from the 1720s until recent times. We find that during the early nineteenth century average height in Portugal did not differ significantly from average height in most other European countries, but that when, around 1850, European anthropometric values began to climb sharply, Portugal's did not. In a panel analysis of 12 countries, we find that delay in human‐capital formation was the chief factor hindering any improvement in the biological standard of living in Portugal.
Visual target detection is impaired at event boundaries
2012-07-30

Boundaries between meaningful events are key moments in comprehending human action. At these points, viewers may focus on the event's contents at the expense of other information. We tested whether visual detection was impaired at those moments perceivers judged to be boundaries between events. Short animated football clips were used as stimulus material, and event boundaries were imposed by having the ball change possession. In a first experiment, we found that possession changes were perceived to be event boundaries. In a second experiment, participants were asked to keep track of 4 of 10 players and to watch for 120 ms probes appearing either at an event boundary or a nonboundary. Probe detection was less accurate at event boundaries. This result suggests that the segmentation of ongoing activity into events corresponds with the regulation of attention over time.
Motion correspondence in the Ternus display shows feature bias in spatiotopic coordinates
2012-07-30

How is the visual system able to maintain object identity as the objects or the eyes move? While many early studies have shown small or no influence of feature information on this correspondence process, more recent studies have shown large feature effects. Here we investigated if this incongruity might be due to the distance over which the feature influence has an effect. We used a variation of the Ternus display (Ternus, 1926), an ambiguous apparent motion display, in which two sets of three discs are presented and one can perceive either three discs moving together (group motion) or one disc jumping across the other two discs (element motion). We biased the percept toward element motion by matching the features of some of the discs. In Experiment 1, with the three discs aligned and moving vertically, we added a horizontal offset between the two sets of discs and found a strong bias toward element motion that decreased with increasing spatial offset. In Experiment 3 participants had to make horizontal saccades across the same Ternus displays so that the two Ternus frames were horizontally offset on the retina, but not in spatiotopic coordinates. We found that the bias showed a similar spatial range, but now it was clear that the range was set in spatial coordinates independently of the retinal position. These results show that feature information contributes to correspondence over a limited spatial range (Experiment 1) and that the range is imposed in spatial, not retinal, coordinates (Experiment 2).
Multi-frequency study of supernova remnants in the Large Magellanic Cloud
2012-07-30

We present new X-ray and radio data of the LMC SNR candidate DEM L205, obtained by XMM-Newton and ATCA, along with archival optical and infrared observations. We use data at various wavelengths to study this object and its complex neighbourhood, in particular in the context of the star formation activity, past and present, around the source. We analyse the X-ray spectrum to derive some remnant's properties, such as age and explosion energy. Supernova remnant features are detected at all observed wavelengths: soft and extended X-ray emission is observed, arising from a thermal plasma with a temperature kT between 0.2 keV and 0.3 keV. Optical line emission is characterised by an enhanced [SII]/Halpha ratio and a shell-like morphology, correlating with the X-ray emission. The source is not or only tentatively detected at near-infrared wavelengths (< 10 microns), but there is a detection of arc-like emission at mid and far-infrared wavelengths (24 and 70 micron) that can be unambiguously associated with the remnant. We suggest that thermal emission from dust heated by stellar radiation and shock waves is the main contributor to the infrared emission. Finally, an extended and faint non-thermal radio emission correlates with the remnant at other wavelengths and we find a radio spectral index between -0.7 and -0.9, within the range for SNRs. The size of the remnant is ~79x64 pc and we estimate a dynamical age of about 35000 years. We definitely confirm DEM L205 as a new SNR. This object ranks amongst the largest remnants known in the LMC. The numerous massive stars and the recent outburst in star formation around the source strongly suggest that a core-collapse supernova is the progenitor of this remnant. (abridged)
Direct current superconducting quantum interferometers with asymmetric shunt resistors
2012-07-30

We have investigated asymmetrically shunted Nb/Al-AlO /Nb direct current\\n(dc) superconducting quantum interference devices (SQUIDs). While keeping the\\ntotal resistance identical to a comparable symmetric SQUID with , we shunted only one of the two Josephson junctions with\\n . Simulations predict that the optimum energy resolution\\n and thus also the noise performance of such an asymmetric SQUID can\\nbe 3--4 times better than that of its symmetric counterpart. Experiments at a\\ntemperature of 4.2\\\\,K yielded for an asymmetric\\nSQUID with an inductance of . For a comparable symmetric device\\n was achieved, confirming our simulation results.\\n
Insulin Resistant Phenotype of Polycystic Ovary Syndrome does not Seem to be Caused by Variation in FTO
2012-07-30

Genetic variation in the FTO gene is associated with increased body weight and reduced insulin sensitivity. We investigated whether genetic variation in FTO is associated with polycystic ovary syndrome (PCOS), a condition also characterized by insulin resistance. Furthermore, we tested whether insulin resistance is specifically associated with genetic variation in FTO in women with PCOS. Sixty-two nondiabetic patients with PCOS defined by the Rotterdam criteria were compared to BMI and age-matched women. Each PCOS case was matched to 2 controls. All participants underwent an oral glucose tolerance test and were genotyped for the single nucleotide polymorphism rs8050136 in the FTO gene. There was no difference in the frequency of FTO genotypes between the PCOS and the non-PCOS groups. In non-PCOS participants, genetic variation in FTO is associated with insulin sensitivity (p=0.03). This association remained significant after adjustment for age and/or BMI (p<= 0.03). In subjects with PCOS, however, FTO did not associate with insulin sensitivity (p=0.67). Genetic variation in FTO does not have an impact on insulin sensitivity in women with PCOS and is therefore not involved in the pathogenesis of the insulin resistant phenotype seen in patients with PCOS.
Neutron background simulation for the CRESST–II experiment
2012-07-30

The CRESST collaboration reported an excess signal in their latest physics run. After removal of expected electromagnetic background, low energy αs and degraded lead recoils from the signal region, a mean value of 35.4 excess events remain. In this work, we investigate if neutron induced nuclear recoils can explain the reported excess. Three results are found: The total event rate in the simulation of 2.04+0.23−0.15 × 10−3 cts /kgd is much lower than the one inferred from the remaining excess events of 4.85 × 10−2 cts /kgd in the experimental data. Additionally, the dominance of oxygen recoils (∼ 90 %) predicted by the simulation is in disagreement with the favored experimental lightyield distribution of the excess signal. Furthermore, the experimentally observed fraction of higher multiplicities is only half of the ∼ 20 % obtained by the simulation. Especially the experimental absence of double detector hits in the presence of higher multiplicities is in clear contradiction to the results of the simulation. In combination, these three discrepancies between the experimental and the simulated background allows the conclusion that the observed excess signal cannot be explained by neutron induced nuclear recoils alone.
Latest results from the CRESST-II Dark Matter Search
2012-07-30

The CRESST-II experiment is searching for Dark Matter particles in the form of WIMPs via their elastic scattering off nuclei in a target material.The CRESST target consists of scintillating CaWO4 crystals which are operated as cryogenic calorimeters at millikelvin temperatures and read out by transition edge sensors.Each interaction in CaWO4 produces a phonon signal in the target crystal and also a light signal that is measured by a secondary cryogenic calorimeter, allowing a very efficient discrimination between electron recoils from radioactive e/γ background and nuclear recoils.Moreover, to some extent, the different types of recoiling nuclei (O, Ca, W) can be distinguished.In the paper we present the latest results of the experiment, obtained from a net exposure of 730kg days acquired with 8 detectors between July 2009 and March 2011.The data has shown a considerable number of events in our signal region.Since this large number of events is not consistent with the known sources of background in our experiment, we discuss the compatibility of this excess of events with a possible WIMP-signal.
On the Grammar of Optative Constructions
2012-07-31

This monograph is one of the first theoretical studies of optatives. Optative constructions express desire without an overt lexical item that means ‘desire’. The author specifically investigates optatives with the syntax of embedded clauses that contain prototypical particles such as ‘only’. He rejects the view that optativity arises compositionally from the standard semantics of embedded clauses and prototypical particles. The following system is proposed: Desirability is due to a generalized scalar exclamation operator EX. Furthermore, clausal properties such as factivity/counterfactuality are encoded in a Mood head, which co-determines morphological mood and complementizer choice. Finally, the prototypical particles that optatives contain are truth-conditionally vacuous presupposition triggers. As a result, these meaning components do not interact directly, but their meanings converge, with the consequence that they prototypically co-occur. This monograph is of interest for formal semanticists, syntacticians, pragmaticists and morphologists, and especially relevant for research on mood and particle semantics.