julilili42/papers huggingface dataset:
Precision measurements with photon-subtracted or photon-added Gaussian states
2014-07-16

Photon-subtracted and photon-added Gaussian states are amongst the simplest non-Gaussian states that are experimentally available. It is generally believed that they are some of the best candidates to enhance sensitivity in parameter extraction. We derive here the quantum Cramér-Rao bound for such states and find that for large photon numbers photon subtraction or addition only leads to a small correction of the quantum Fisher information (QFI). On the other hand, a divergence of the QFI appears for very small squeezing in the limit of vanishing photon number in the case of photon subtraction, implying an arbitrarily precise measurement with almost no light. However, at least for the standard and experimentally established preparation scheme, the decreasing success probability of the preparation in that limit exactly cancels the divergence, leading to finite sensitivity per square root of Hz, when the duration of the preparation is taken into account.
Red fluorescence increases with depth in reef fishes, supporting a visual function, not UV protection
2014-07-16

Why do some marine fishes exhibit striking patterns of natural red fluorescence? In this study, we contrast two non-exclusive hypotheses: (i) that UV absorption by fluorescent pigments offers significant photoprotection in shallow water, where UV irradiance is strongest; and (ii) that red fluorescence enhances visual contrast at depths below −10 m, where most light in the ‘red’ 600–700 nm range has been absorbed. Whereas the photoprotection hypothesis predicts fluorescence to be stronger near the surface and weaker in deeper water, the visual contrast hypothesis predicts the opposite. We used fluorometry to measure red fluorescence brightness in vivo in individuals belonging to eight common small reef fish species with conspicuously red fluorescent eyes. Fluorescence was significantly brighter in specimens from the −20 m sites than in those from −5 m sites in six out of eight species. No difference was found in the remaining two. Our results support the visual contrast hypothesis. We discuss the possible roles fluorescence may play in fish visual ecology and highlight the possibility that fluorescent light emission from the eyes in particular may be used to detect cryptic prey.
Island size evolution and molecular diffusion during growth of organic thin films followed by time-resolved specular and off-specular scattering
2014-07-16

We report on a combined off-specular and specular x-ray scattering growth study of ultrathin films of the prototypical organic semiconductor diindenoperylene (DIP, C32H16). We investigate the evolution of the in-plane correlation length and the growth kinetics of the films including their dependence on the substrate temperature and the growth rate. We observe a temperature-dependent collective rearrangement of DIP molecules from a transient surface induced to the thin-film phase, which can be rationalized by incorporating a thickness-dependent out-of-plane lattice parameter. We further observe that the nucleation behavior of DIP changes from the first to the second monolayer, which we relate to a difference in the diffusion length of the molecules.
The low energy signaling network
2014-07-17

Stress impacts negatively on plant growth and crop productivity, caicultural production worldwide. Throughout their life, plants are often confronted with multiple types of stress that affect overall cellular energy status and activate energy-saving responses. The resulting low energy syndrome (LES) includes transcriptional, translational, and metabolic reprogramming and is essential for stress adaptation. The conserved kinases sucrose-non-fermenting-1-related protein kinase-1 (SnRK1) and target of rapamycin (TOR) play central roles in the regulation of LES in response to stress conditions, affecting cellular processes and leading to growth arrest and metabolic reprogramming. We review the current understanding of how TOR and SnRK1 are involved in regulating the response of plants to low energy conditions. The central role in the regulation of cellular processes, the reprogramming of metabolism, and the phenotypic consequences of these two kinases will be discussed in light of current knowledge and potential future developments.
Morphology Related Photodegradation of Low‐Band‐Gap Polymer Blends
2014-07-17

The morphology related photodegradation of low band‐gap polymer blends is investigated using optical microscopy and scanning probe microscopy. Poly[2,6‐(4,4‐bis‐(2‐ethylhexyl)‐4H‐cyclopenta[2,1‐b;3,4‐b′]dithiophene)‐alt‐4,7(2,1,3‐benzothiadiazole)] (C‐PCPDTBT):[6,6]‐phenyl C61‐butyric acid methyl ester (PCBM) blend films without and with ODT, as well as poly[(4,40‐bis(2‐ethylhexyl)dithieno[3,2‐b:20,30‐d]silole)‐2,6‐diylalt‐(2,1,3‐benzothiadiazole)‐4,7‐diyl] (Si‐PCPDTBT):PCBM blend films exposed to a focused 632.8 nm laser under ambient condition with and without inert gas protection are studied. The photodegradation of the polymer starts in the vicinity of the PCBM molecules (first sphere degradation), which effectively blocks the electron transfer processes. Stern‐Volmer type kinetics are observed in the C‐PCPDTBT:PCBM blend with ODT, which indicates that only a small number of photo‐oxidized monomer units act as quenchers of the C‐PCPDTBT polymer luminescence. Furthermore, in addition to the permanent damage of the polymer molecules, as witnessed from their Raman intensity decrease, the polymer photoluminescence demonstrates partial reversible recovery when inert gas protection is resumed, indicating the involvement of temporary polymer/O 2 ‐charge transfer complexes in the photodegradation process.
Bacteriophage-Based Latex Agglutination Test for Rapid Identification of Staphylococcus aureus
2014-07-17

ABSTRACT Rapid diagnosis is essential for the management of Staphylococcus aureus infections. A host recognition protein from S. aureus bacteriophage phiSLT was recombinantly produced and used to coat streptavidin latex beads to develop a latex agglutination test (LAT). The diagnostic accuracy of this bacteriophage-based test was compared with that of a conventional LAT, Pastorex Staph-Plus, by investigating a clinical collection of 86 S. aureus isolates and 128 coagulase-negative staphylococci (CoNS) from deep tissue infections. All of the clinical S. aureus isolates were correctly identified by the bacteriophage-based test. While most of the CoNS were correctly identified as non- S. aureus isolates, 7.9% of the CoNS caused agglutination. Thus, the sensitivity of the bacteriophage-based LAT for identification of S. aureus among clinical isolates was 100%, its specificity was 92.1%, its positive predictive value (PPV) was 89.6%, and its negative predictive value (NPV) was 100%. The sensitivity, specificity, PPV, and NPV of the Pastorex LAT for the identification of S. aureus were 100%, 99.2%, 98.9%, and 100%, respectively. Among the additionally tested 35 S. aureus and 91 non- S. aureus staphylococcal reference and type strains, 1 isolate was false negative by each system; 13 and 8 isolates were false positive by the bacteriophage-based and Pastorex LATs, respectively. The ability of the phiSLT protein to detect S. aureus was dependent on the presence of wall teichoic acid (WTA) and corresponded to the production of ribitol phosphate WTA, which is found in most S. aureus clones but only a small minority of CoNS. Bacteriophage-based LAT identification is a promising strategy for rapid pathogen identification. Finding more specific bacteriophage proteins would increase the specificity of this novel diagnostic approach.
Euclidean Minimal Tori with Planar Ends and Elliptic Solitons
2014-07-17

A Euclidean minimal torus with planar ends gives rise to an immersed Willmore torus in the conformal 3-sphere &lt;f&gt; &lt;/f&gt;. The class of Willmore tori obtained this way is given a spectral theoretic characterization as the class of Willmore tori with reducible spectral curve. A spectral curve of this type is necessarily the double of the spectral curve of an elliptic Kadomtsev-Petviashvili (KP) soliton. The simplest possible examples of minimal tori with planar ends are related to 1-gap Lamé potentials, the simplest nontrivial algebro geometric Korteweg-de Vries (KdV) potentials. If one allows for translational periods, Riemann's “staircase” minimal surfaces appear as other examples related to 1-gap Lamé potentials.
Late Holocene primary productivity and sea surface temperature variations in the northeastern Arabian Sea: Implications for winter monsoon variability
2014-07-18

Variability in the oceanic environment of the Arabian Sea region is strongly influenced by the seasonal monsoon cycle of alternating wind directions. Prominent and well studied is the summer monsoon, but much less is known about late Holocene changes in winter monsoon strength with winds from the northeast that drive convective mixing and high surface ocean productivity in the northeastern Arabian Sea. To establish a high-resolution record of winter monsoon variability for the late Holocene, we analyzed alkenone-derived sea surface temperature (SST) variations and proxies of primary productivity (organic carbon and δ15N) in a well-laminated sediment core from the Pakistan continental margin. Weak winter monsoon intensities off Pakistan are indicated from 400 B.C. to 250 A.D. by reduced productivity and relatively high SST. At about 250 A.D., the intensity of the winter monsoon increased off Pakistan as indicated by a trend to lower SST. We infer that monsoon conditions were relatively unstable from ~500 to 1300 A.D., because primary production and SST were highly variable. Declining SST and elevated biological production from 1400 to 1900 A.D. suggest invigorated convective winter mixing by strengthening winter monsoon circulation, most likely a regional expression of colder climate conditions during the Little Ice Age on the Northern Hemisphere. The comparison of winter monsoon intensity with records of summer monsoon intensity suggests that an inverse relationship between summer and winter monsoon strength exists in the Asian monsoon system during the late Holocene, effected by shifts in the Intertropical Convergence Zone.
A general non-linear multilevel structural equation mixture model
2014-07-18

In the past 2 decades latent variable modeling has become a standard tool in the social sciences. In the same time period, traditional linear structural equation models have been extended to include non-linear interaction and quadratic effects (e.g., Klein and Moosbrugger, 2000), and multilevel modeling (Rabe-Hesketh et al., 2004). We present a general non-linear multilevel structural equation mixture model (GNM-SEMM) that combines recent semiparametric non-linear structural equation models (Kelava and Nagengast, 2012; Kelava et al., 2014) with multilevel structural equation mixture models (Muthén and Asparouhov, 2009) for clustered and non-normally distributed data. The proposed approach allows for semiparametric relationships at the within and at the between levels. We present examples from the educational science to illustrate different submodels from the general framework.
ERBB4 Promoter Polymorphism Is Associated with Poor Distant Disease-Free Survival in High-Risk Early Breast Cancer
2014-07-18

A number of genetic variants have been linked to increased risk of breast cancer. Little is, however, known about the prognostic significance of hereditary factors. Here, we investigated the frequency and prognostic significance of two ERBB4 promoter region variants, -782G>T (rs62626348) and -815A>T (rs62626347), in a cohort of 1010 breast cancer patients. The frequency of nine previously described somatic ERBB4 kinase domain mutations was also analyzed. Clinical material used in the study consisted of samples from the phase III, adjuvant, FinHer breast cancer trial involving 1010 women. Tumor DNA samples were genotyped for ERBB4 variants and somatic mutations using matrix-assisted laser desorption ionization/time of flight mass spectrometry. Paraffin-embedded tumor sections from all patients were immunohistochemically stained for ErbB4 expression. Association of ERBB4 genotype to distant disease-free survival (DDFS) was assessed using Kaplan-Meier and Cox regression analyses. Genotyping was successful for 91-93% of the 1010 samples. Frequencies observed for the ERBB4 variants were 2.5% and 1.3% for -782G>T and -815A>T, respectively. Variant -815A>T was significantly associated with poor survival (HR = 2.86 [95% CI 1.15-6.67], P = 0.017). In contrast, variant -782G>T was associated with well-differentiated cancer (P = 0.019). Two (0.2%) ERBB4 kinase domain mutations were found, both of which have previously been shown to be functional and promote cancer cell growth in vitro. These data present the germ-line ERBB4 variant -815A>T as a novel prognostic marker in high-risk early breast cancer and indicate the presence of rare but potentially oncogenic somatic ERBB4 mutations in breast cancer.
Neurosharing: large-scale data sets (spike, LFP) recorded from the hippocampal-entorhinal system in behaving rats
2014-07-18

Using silicon-based recording electrodes, we recorded neuronal activity of the dorsal hippocampus and dorsomedial entorhinal cortex from behaving rats. The entorhinal neurons were classified as principal neurons and interneurons based on monosynaptic interactions and wave-shapes. The hippocampal neurons were classified as principal neurons and interneurons based on monosynaptic interactions, wave-shapes and burstiness. The data set contains recordings from 7,736 neurons (6,100 classified as principal neurons, 1,132 as interneurons, and 504 cells that did not clearly fit into either category) obtained during 442 recording sessions from 11 rats (a total of 204.5 hours) while they were engaged in one of eight different behaviours/tasks. Both original and processed data (time stamp of spikes, spike waveforms, result of spike sorting and local field potential) are included, along with metadata of behavioural markers. Community-driven data sharing may offer cross-validation of findings, refinement of interpretations and facilitate discoveries.
Abstract 62: The Coxsackie Virus B3 modulates Cardiac Ion Channels
2014-07-18

Infections with coxsackieviruses of type B (CVB) induce severe forms of acute and chronic myocarditis that are often accompanied by ventricular arrhythmias. The mechanisms underlying the development of virus-induced, life-threatening arrhythmia, remain largely elusive. Here, we show time-dependent CVB3-induced modulation of the cardiac ion channels Kv7.1, hERG1 and CaV1.2 in vitro. Channel protein localizations within cells and plasma membrane abundance are altered in infected mouse cardiac cells. In silico analyses of infected human myocytes suggest increased risk of arrhythmogenesis. These modifications are attenuated by the common Asian polymorphism KCNQ1-P448R, a genetic determinant preventing coxsackievirus-induced effects in vitro. This study provides a previously unknown explanation for the development of arrhythmias in enteroviral myocarditis, which will help to develop therapeutic strategies for arrhythmia treatment.
Abstract 63: Potential Genetic and Pharmacological Protection from Virus-induced Ventricular Arrhythmias and Sudden Cardiac Death
2014-07-18

In patients as well as in mouse models, enteroviral infections, especially Coxsackie group B viruses (CVB1-6), frequently induce ventricular arrhythmias and sudden cardiac death. The cardiac action potential requires proper function of cardiac ion channels. CVB3 alters Kv7.1 channel trafficking potentially leading to changes in action potentials and increasing likelihood of arrhythmias. Genetic variants of cardiac ion channels can cause changes in channel trafficking that may preserve from CVB3 modulations and present an evolutionary advantage. Here, we show that a common polymorphic Kv7.1 channel variant uses alternative trafficking pathways and may thus exert a benefit during CVB3 infections. Genetic and pharmacological disruption of a CVB3-stimulated Serum- and Glucocorticoid inducible Kinase 1 (SGK1) pathways blunts Kv7.1 channel dysfunctions. Our results suggest that escape from CVB3-induced SGK1-stimulation by genetic variation in Kv7.1 may be protective and inhibition of SGK1 may present a pharmacological approach to reduce the pro-arrhythmic risk associated with acute coxsackievirus infections.
Integrative and Personalized QSAR Analysis in Cancer by Kernelized Bayesian Matrix Factorization
2014-07-21

With data from recent large-scale drug sensitivity measurement campaigns, it is now possible to build and test models predicting responses for more than one hundred anticancer drugs against several hundreds of human cancer cell lines. Traditional quantitative structure-activity relationship (QSAR) approaches focus on small molecules in searching for their structural properties predictive of the biological activity in a single cell line or a single tissue type. We extend this line of research in two directions: (1) an integrative QSAR approach predicting the responses to new drugs for a panel of multiple known cancer cell lines simultaneously and (2) a personalized QSAR approach predicting the responses to new drugs for new cancer cell lines. To solve the modeling task, we apply a novel kernelized Bayesian matrix factorization method. For maximum applicability and predictive performance, the method optionally utilizes genomic features of cell lines and target information on drugs in addition to chemical drug descriptors. In a case study with 116 anticancer drugs and 650 cell lines, we demonstrate the usefulness of the method in several relevant prediction scenarios, differing in the amount of available information, and analyze the importance of various types of drug features for the response prediction. Furthermore, after predicting the missing values of the data set, a complete global map of drug response is explored to assess treatment potential and treatment range of therapeutically interesting anticancer drugs.
An Fc‐optimized NKG2D‐immunoglobulin G fusion protein for induction of natural killer cell reactivity against leukemia
2014-07-21

Recruitment of Fc‐receptor‐bearing effector cells, such as natural killer (NK) cells, is a feature critical for the therapeutic success of antitumor antibodies and can be improved by the modifications of an antibody's Fc part. The various ligands of the activating immunoreceptor NKG2D, NKG2DL) are selectively expressed on malignant cells including leukemia. We here took advantage of the tumor‐associated expression of NKG2DL for targeting leukemic cells by NKG2D–immunoglobulin G (IgG)1 fusion proteins containing modified Fc parts. Compared to NKG2D–Fc containing a wild‐type Fc part (NKG2D–Fc–WT), our mutants (S239D/I332E and E233P/L234V/L235A/ΔG236/A327G/A330S) displayed highly enhanced (NKG2D–Fc–ADCC) and abrogated (NKG2D–Fc–KO) affinity to the NK cell Fc receptor, respectively. Functional analyses with allogenic as well as autologous NK cells and primary malignant cells of leukemia patients revealed that NKG2D–Fc–KO significantly reduced NK reactivity by blocking immunostimulatory NKG2D–NKG2DL interaction. NKG2D–Fc–WT already enhanced antileukemia reactivity by inducing antibody‐dependent cellular cytotoxicity (ADCC) with NKG2D–Fc–ADCC mediating significantly stronger effects. Parallel application of NKG2D–Fc–ADCC with Rituximab caused additive effects in lymphoid leukemia. In line with the tumor‐associated expression of NKG2DL, no NK cell ADCC against resting healthy blood cells was induced. Thus, NKG2D–Fc–ADCC potently enhances NK antileukemia reactivity despite the inevitable reduction of activating signals upon binding to NKG2DL and may constitute an attractive means for immunotherapy of leukemia.
Predominance of Biotic over Abiotic Formation of Halogenated Hydrocarbons in Hypersaline Sediments in Western Australia
2014-07-21

Volatile halogenated organic compounds (VOX) contribute to ozone depletion and global warming. There is evidence of natural VOX formation in many environments ranging from forest soils to salt lakes. Laboratory studies have suggested that VOX formation can be chemically stimulated by reactive Fe species while field studies have provided evidence for direct biological (enzymatic) VOX formation. However, the relative contribution of abiotic and biotic processes to global VOX budgets is still unclear. The goals of this study were to quantify VOX release from sediments from a hypersaline lake in Western Australia (Lake Strawbridge) and to distinguish between the relative contributions of biotic and abiotic VOX formation in microbially active and sterilized microcosms. Our experiments demonstrated that the release of organochlorines from Lake Strawbridge sediments was mainly biotic. Among the organochlorines detected were monochlorinated, e.g., chloromethane (CH3Cl), and higher chlorinated VOX compounds such as trichloromethane (CHCl3). Amendment of sediments with either Fe(III) oxyhydroxide (ferrihydrite) or a mixture of lactate/acetate or both ferrihydrite and lactate/acetate did not stimulate VOX formation. This suggests that although microbial Fe(III) reduction took place, there was no stimulation of VOX formation via Fe redox transformations or the formation of reactive Fe species under our experimental conditions.
Constraining white dwarf viscosity through tidal heating in detached binary systems
2014-07-21

Although the internal structure of white dwarfs is considered to be generally\\nwell understood, the source and entity of viscosity is still very uncertain. We\\npropose here to study white dwarf viscous properties using short period (&lt; 1\\nhr), detached white dwarf binaries, such as the newly discovered ~12.8 min\\nsystem. These binaries are wide enough that mass transfer has not yet started\\nbut close enough that the least massive component is subject to a measurable\\ntidal deformation. The associated tidal torque transfers orbital energy, which\\nis partially converted into heat by the action of viscosity within the deformed\\nstar. As a consequence, its outer non-degenerate layers expand, and the star\\npuffs up. We self-consistently calculate the fractional change in radius, and\\nthe degree of asynchronism (ratio of stellar to orbital spin) as a function of\\nthe viscous time. Specializing our calculations to J0651, we find that the\\ndiscrepancy between the measured radius of the secondary star and He white\\ndwarf model predictions can be interpreted as tidal inflation if the viscous\\ntimescale is either ~2 10^5 yr or ~10^4 yr. Such values point to a\\nnon-microscopic viscosity, possibly given by tidally induced turbulence, or by\\nmagnetic field stresses with a magnetic field strength of 10-100 Gauss.\\nFortunately, these two timescales produce very different degree of\\nasynchronism, with the shortest one, bringing the system much closer to\\nsynchronisation. A measurement of the stellar spin can thus univocally\\ndetermined the mean viscosity. Extrapolating the secondary's radial expansion,\\nwe predict that the star will fill is Roche lobe at a separation which is\\n1.2-1.3 smaller than the current one. Applying this method to a future sample\\nof systems can allow us to learn whether viscosity changes with mass and/or\\nnuclear composition.\\n