julilili42/papers huggingface dataset:
Enhancement of Radiative Plasmon Decay by Hot Electron Tunneling
2015-07-22

Here we demonstrate that photon emission induced by inelastic tunneling through a nanometer single gap between a sharp Au tip and an Au substrate can be significantly enhanced by the illumination of the junction with 634 nm laser light with an electric field component oriented parallel to the tip-axis, i.e., perpendicular to the sample. Analyzing photoluminescence (PL) spectra recorded as a function of bias voltage allows us to distinguish between PL from (1) the decay of electron-hole pairs created by the laser excited sp/d interband transition with a characteristic band at 690 nm and (2) the red-shifted radiative decay of characteristic plasmon modes formed by the gap. Since the electroluminescence spectra (without laser) already show the plasmonic gap modes, we conclude that the enhanced intensity induced by laser illumination originates from the radiative decay of hot electrons closely above the Fermi level via inelastic tunneling and photon emission into the plasmon modes. Since these processes can be independently controlled by laser illumination and the amplitude of the bias voltage, it is of great interest for designing new switchable photon emission plasmonic devices.
Motion of Magnetic Flux Quanta in Type-II Superconductors – Some Open Questions
2015-07-22

Abstract The motion of the magnetic flux quanta in the mixed state of a type-II superconductor, due to the Lorentz force of an electric transport current, represents the key mechanism for generating resistive losses. Whereas the most common result is Joule heating of the superconductor, also purely electronic non-equilibrium effects can play a dominant role in the case of effective cooling of the sample. The latter situation can be realized by means of very thin superconducting films (having a large surface/ volume ratio). In this paper we discuss experiments with Nd2−xCexCuOy (NCCO) films performed some time ago, yielding evidence for electronic non-equilibrium effects due to the energy dependence of the quasi-particle density of states in the mixed state of the films. The films were imbedded within super-fluid helium for cooling. The recent advances in the fabrication of epitaxial ultra-thin superconducting films promise to contribute to further clarification of these electronic non-equilibrium effects.
Acoustic behavior of melon-headed whales varies on a diel cycle
2015-07-23

Many terrestrial and marine species have a diel activity pattern, and their acoustic signaling follows their current behavioral state. Whistles and echolocation clicks on long-term recordings produced by melon-headed whales (<i>Peponocephala electra</i>) at Palmyra Atoll indicated that these signals were used selectively during different phases of the day, strengthening the idea of nighttime foraging and daytime resting with afternoon socializing for this species. Spectral features of their echolocation clicks changed from day to night, shifting the median center frequency up. Additionally, click received levels increased with increasing ambient noise during both day and night. Ambient noise over a wide frequency band was on average higher at night. The diel adjustment of click features might be a reaction to acoustic masking caused by these nighttime sounds. Similar adaptations have been documented for numerous taxa in response to noise. Or it could be, unrelated, an increase in biosonar source levels and with it a shift in center frequency to enhance detection distances during foraging at night. Call modifications in intensity, directionality, frequency, and duration according to echolocation task are well established for bats. This finding indicates that melon-headed whales have flexibility in their acoustic behavior, and they collectively and repeatedly adapt their signals from day- to nighttime circumstances.
An artificial elementary eye with optic flow detection and compositional properties
2015-07-23

We describe a 2 mg artificial elementary eye whose structure and functionality is inspired by compound eye ommatidia. Its optical sensitivity and electronic architecture are sufficient to generate the required signals for the measurement of local optic flow vectors in multiple directions. Multiple elementary eyes can be assembled to create a compound vision system of desired shape and curvature spanning large fields of view. The system configurability is validated with the fabrication of a flexible linear array of artificial elementary eyes capable of extracting optic flow over multiple visual directions.
Contribution of working memory in multiplication fact network in children may shift from verbal to visuo-spatial: a longitudinal investigation
2015-07-23

Number facts are commonly assumed to be verbally stored in an associative multiplication fact retrieval network. Prominent evidence for this assumption comes from so-called operand-related errors (e.g., 4 × 6 = 28). However, little is known about the development of this network in children and its relation to verbal and non-verbal memories. In a longitudinal design, we explored elementary school children from grades 3 and 4 in a multiplication verification task with the operand-related and -unrelated distractors. We examined the contribution of multiplicative fact retrieval by verbal and visuo-spatial short-term and working memory (WM). Children in grade 4 showed smaller reaction times in all conditions. However, there was no significant difference in errors between grades. Contribution of verbal and visuo-spatial WM also changed with grade. Multiplication correlated with verbal WM and performance in grade 3 but with visuo-spatial WM and performance in grade 4. We suggest that the relation to verbal WM in grade 3 indicates primary linguistic learning of and access to multiplication in grade 3 which is probably based on verbal repetition of the multiplication table heavily practiced in grades 2 and 3. However, the relation to visuo-spatial semantic WM in grade 4 suggests that there is a shift from verbal to visual and semantic learning in grade 4. This shifting may be induced because later in elementary school, multiplication problems are rather carried out via more written, i.e., visual tasks, which also involve executive functions. More generally, the current data indicates that mathematical development is not generally characterized by a steady progress in performance; rather verbal and non-verbal memory contributions of performance shift over time, probably due to different learning contents.
Effects of Irregular Bimetallic Nanostructures on the Optical Properties of Photosystem I from Thermosynechococcus elongatus
2015-07-23

The fluorescence of photosystem I (PSI) trimers in proximity to bimetallic plasmonic nanostructures have been explored by single-molecule spectroscopy (SMS) at cryogenic temperature (1.6 K). PSI serves as a model for biological multichromophore-coupled systems with high potential for biotechnological applications. Plasmonic nanostructures are fabricated by thermal annealing of thin metallic films. The fluorescence of PSI has been intensified due to the coupling with plasmonic nanostructures. Enhancement factors up to 22.9 and 5.1 are observed for individual PSI complexes coupled to Au/Au and Ag/Au samples, respectively. Additionally, a wavelength dependence of fluorescence enhancement is observed, which can be explained by the multichromophoric composition of PSI.
Efimov Resonance and Three-Body Parameter in a Lithium-Rubidium Mixture
2015-07-24

We study collisional heating in a cold ^{7}Li-^{87}Rb mixture near a broad Feshbach resonance at 661 G. At the high field slope of the resonance, we find an enhanced three-body recombination rate that we interpret as a heteronuclear Efimov resonance. With improved Feshbach spectroscopy of two further resonances, a model for the molecular potentials has been developed that now consistently explains all known Feshbach resonances of the various Li-Rb isotope mixtures. The model is used to determine the scattering length of the observed Efimov state. Its value of -1870a_{0} Bohr radii supports the currently discussed assumption of universality of the three-body parameter also in heteronuclear mixtures.
All-optical measurement of Rydberg-state lifetimes
2015-07-24

We have developed an all-optical method for measuring the lifetimes of \\nand Rydberg states and demonstrate its capabilities with measurements on\\na dilute cloud of ultracold Rb atoms in a cryogenic environment. The\\nmethod is based on the time-resolved observation of resonant light absorption\\nby ground state atoms and selective transfer of Rydberg atoms into the ground\\nstate at varying delay times in order to reconstruct Rydberg decay curves. Our\\nmeasurements of the Rb state indicate an increase of the\\nlifetime at lowered environment temperatures, as expected due to decreased\\nblack body radiation. For the state with an attractive\\ndipole-dipole interaction, ionization and lifetime reduction due to collisional\\neffects are observed.\\n
Regulation of the perilymphatic–endolymphatic water shunt in the cochlea by membrane translocation of aquaporin-5
2015-07-24

Volume homeostasis of the cochlear endolymph depends on radial and longitudinal endolymph movements (LEMs). LEMs measured in vivo have been exclusively recognized under physiologically challenging conditions, such as experimentally induced alterations of perilymph osmolarity or endolymph volume. The regulatory mechanisms that adjust LEMs to the physiological requirements of endolymph volume homeostasis remain unknown. Here, we describe the formation of an aquaporin (AQP)-based "water shunt" during the postnatal development of the mouse cochlea and its regulation by different triggers. The final complementary expression pattern of AQP5 (apical membrane) and AQP4 (basolateral membrane) in outer sulcus cells (OSCs) of the cochlear apex is acquired at the onset of hearing function (postnatal day (p)8-p12). In vitro, hyperosmolar perfusion of the perilymphatic fluid spaces or the administration of the muscarinic agonist pilocarpine in cochlear explants (p14) induced the translocation of AQP5 channel proteins into the apical membranes of OSCs. AQP5 membrane translocation was blocked by the muscarinic antagonist atropine. The muscarinic M3 acetylcholine (ACh) receptor (M3R) was identified in murine OSCs via mRNA expression, immunolabeling, and in vitro binding studies using an M3R-specific fluorescent ligand. Finally, the water shunt elements AQP4, AQP5, and M3R were also demonstrated in OSCs of the human cochlea. The regulation of the AQP4/AQP5 water shunt in OSCs of the cochlear apex provides a molecular basis for regulated endolymphatic volume homeostasis. Moreover, its dysregulation or disruption may have pathophysiologic implications for clinical conditions related to endolymphatic hydrops, such as Ménière's disease.
Ultrasensitive Label-Free Immunoassay for Optical Determination of Amitriptyline and Related Tricyclic Antidepressants in Human Serum
2015-07-24

The present work focuses on the development of a label-free and ultrasensitive immunoassay for the detection of the drug amitriptyline in human serum. Reflectometric interference spectroscopy is used as the detection method, providing a simple, but highly sensitive optical setup. Amitriptyline is a common antidepressant; however, it has a small therapeutic window and can cause severe side effects in case of wrong dosage. Therefore, it is highly recommended for therapeutic drug monitoring to control the drug level. The limit of detection for this optical immunosensor was determined in buffer (0.3 μg/L) and in human serum (0.5 μg/L). It has become evident that this assay can compete with HPLC measurements. For drug concentrations at a normal level or above, the sample can be diluted up to 1:100. Especially for limited sample volumes, this is a great advantage. The sensor surface shows very high stability, and together with the regeneration solution 80 measurement cycles can be performed on each transducer chip. Cross-reactivity experiments indicate that a sum determination of several tricyclic antidepressants is possible.
Lower Pre-Treatment T Cell Activation in Early- and Late-Onset Tuberculosis-Associated Immune Reconstitution Inflammatory Syndrome
2015-07-24

Our data provide evidence of reduced CD8+ T cell activation before ART as a common predisposing factor of early- and late-onset TB-IRIS. The occurrence of TB-IRIS itself was not marked by an over-activated CD8+ T cell compartment. Late- but not early-onset TB-IRIS was characterized by a more terminally differentiated T cell phenotype.
High definition urethral pressure profilometry: Evaluating a novel microtip catheter
2015-07-24

Introduction Urethral pressure profilometry (UPP) is used in the diagnosis of stress urinary incontinence (SUI). SUI is a significant medical, social, and economic problem, affecting about 12.5% of the population. A novel microtip catheter was developed for UPP featuring an inclination sensor and higher angular resolution compared to systems in clinical use today. Therewith, the location of each measured pressure sample can be determined and the spatial pressure distribution inside the urethra reconstructed. In order to assess the performance and plausibility of data from the microtip catheter, we compare it to data from a double balloon air charged system. Materials and Methods Both catheters are used on sedated female minipigs. Data from the microtip catheter are processed through a signal reconstruction algorithm, plotted and compared against data from the air‐charged catheter. Results The microtip catheter delivers results in agreement with previous comparisons of microtip and air‐charged systems. It additionally provides a new level of detail in the reconstructed UPPs which may lead to new insights into the sphincter mechanism of minipigs. Conclusions The ability of air‐charged catheters to measure pressure circumferentially is widely considered a main advantage over microtip catheters. However, directional pressure readings can provide additional information on angular fluctuations in the urethral pressure distribution. It is shown that the novel microtip catheter in combination with a signal reconstruction algorithm delivers plausible data. It offers the opportunity to evaluate urethral structures, especially the sphincter, in context of the correct location within the anatomical location of the pelvic floor. Neurourol. Urodynam. 35:888–894, 2016 . © 2015 Wiley Periodicals, Inc.
Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens
2015-07-24

Abstract Herbaria archive a record of changes of worldwide plant biodiversity harboring millions of specimens that contain DNA suitable for genome sequencing. To profit from this resource, it is fundamental to understand in detail the process of DNA degradation in herbarium specimens. We investigated patterns of DNA fragmentation -length and base composition at breaking points-, and nucleotide misincorporation by analyzing 86 herbarium samples spanning the last 300 years using Illumina shot-gun sequencing. We found an exponential decay relationship between DNA fragmentation and time, and estimated a per nucleotide fragmentation rate of 1.66 × 10 −4 per year, which is ten times faster than the rate estimated for fossilized bones. Additionally, we found that strand breaks occur specially before purines, and that depurination-driven DNA breakage occurs constantly through time and can to a great extent explain decreasing fragment length over time. Similar of what has been found analyzing ancient DNA from bones, we found a strong correlation between the deamination-driven accumulation of cytosine (C) to thymine (T) substitutions and time, which reinforces the importance of substitution patterns to authenticate the ancient/historical nature of DNA fragments. Accurate estimations of DNA degradation through time will allow informed decisions about laboratory and computational procedures to take advantage of the vast collection of worldwide herbarium specimens.
Long-term live imaging reveals cytosolic immune responses of host hepatocytes againstPlasmodiuminfection and parasite escape mechanisms
2015-07-25

Plasmodium parasites are transmitted by Anopheles mosquitoes to the mammalian host and actively infect hepatocytes after passive transport in the bloodstream to the liver. In their target host hepatocyte, parasites reside within a parasitophorous vacuole (PV). In the present study it was shown that the parasitophorous vacuole membrane (PVM) can be targeted by autophagy marker proteins LC3, ubiquitin, and SQSTM1/p62 as well as by lysosomes in a process resembling selective autophagy. The dynamics of autophagy marker proteins in individual Plasmodium berghei-infected hepatocytes were followed by live imaging throughout the entire development of the parasite in the liver. Although the host cell very efficiently recognized the invading parasite in its vacuole, the majority of parasites survived this initial attack. Successful parasite development correlated with the gradual loss of all analyzed autophagy marker proteins and associated lysosomes from the PVM. However, other autophagic events like nonselective canonical autophagy in the host cell continued. This was indicated as LC3, although not labeling the PVM anymore, still localized to autophagosomes in the infected host cell. It appears that growing parasites even benefit from this form of nonselective host cell autophagy as an additional source of nutrients, as in host cells deficient for autophagy, parasite growth was retarded and could partly be rescued by the supply of additional amino acid in the medium. Importantly, mouse infections with P. berghei sporozoites confirmed LC3 dynamics, the positive effect of autophagy activation on parasite growth, and negative effects upon autophagy inhibition.
Influence ofOpa1Mutation on Survival and Function of Retinal Ganglion Cells
2015-07-25

Purpose: Mutations in the OPA1 gene cause autosomal dominant optic atrophy (ADOA), a visual disorder associated with degeneration of retinal ganglion cells (RGCs). Here, we characterized the disease progression in a homologous mouse model B6;C3-Opa1329-355del and asked whether the pronounced cell death affects certain RGC types more than others. Methods: The influence of the Opa1 mutation was assessed by morphologic (retina and optic nerve histology) and functional (multielectrode array) methods. Results: The RGC loss of approximately 50% within 18 months was significantly more pronounced in RGCs with small-caliber axons. Small-caliber axon RGCs comprise a variety of functional RGC types. Accordingly, electrophysiological analyses of RGCs did not show a dropout of distinct functional RGC subgroups. However, the response properties of RGCs were affected significantly by the mutation. Surprisingly, these functional changes were different under different luminance conditions (scotopic, mesopic, and photopic). Finally, melanopsin cells are known to be less susceptible to retinal insults. We found that these cells are also spared in the Opa1 mouse model, and demonstrated for the first time that this resistance persisted even when the melanopsin gene had been knocked-out. Conclusions: Small-caliber axons show a higher vulnerability to the Opa1 mutation in our mouse model for ADOA. Luminance-dependent functional changes suggest an influence of the Opa1 mutation on the retinal circuitry upstream of RGCs. Photoresponsive RGCs are protected against cell death due to the Opa1 mutation, but not by melanopsin expression itself.
Quantification of Yttria in Stabilized Zirconia by Raman Spectroscopy
2015-07-26

The relationship between Y 2 O 3 content in tetragonal and cubic ZrO 2 phases and the shift of the Raman band at ∼645/cm was investigated. With increasing Y 2 O 3 content, the 645/cm Raman band position decreases to lower Raman shift values. A fit of x = Y 2 O 3 content in wt% and y = Raman band position in per cm, was found to be valid for low Y 2 O 3 ‐stabilized t‐ZrO 2 , t′′‐ZrO 2 transition, and fully stabilized c‐ZrO 2 . Modeling the change in lattice parameters due to the incorporation of Y 2 O 3 in ZrO 2 as obtained from Rietveld‐refined XRD data confirms that the peculiar sigmoidal form of the band shift with Y 2 O 3 content is mainly due to a variation of the amount of oxygen vacancies. The resultant method is highly attractive in fields of Y 2 O 3 determination in ZrO 2 materials where a fast, spatially resolved, and nondestructive analysis is required.
Endothelial depletion of murine SRF/MRTF provokes intracerebral hemorrhagic stroke
2015-07-28

Significance Human cerebral small vessel disease (SVD) comprises age-associated intracerebral hemorrhages and global cognitive impairment, including vascular dementia. Human SVD presents in either familial or sporadic manifestation, involving either monogenic Mendelian defects or multitrait genetic variants. To better characterize the genetic and molecular mechanisms underlying SVD, appropriate animal models are needed. The Srf iECKO mouse model presented here resembles human SVD pathology with regard to intracerebral hemorrhage formation and vascular dementia, including variability in onset and progression of cerebral symptoms. The Serum Response Factor (SRF)/Myocardin Related Transcription Factor (MRTF) are shown to regulate the expression of genes, which are essential for the maintenance of blood–brain barrier function and cerebral microvessel integrity. These findings suggest impairment of SRF/MRTF-mediated gene control as a molecular mechanism contributing to human SVD.
In vivoprotein crystallization in combination with highly brilliant radiation sources offers novel opportunities for the structural analysis of post-translationally modified eukaryotic proteins
2015-07-28

During the last decade, the number of three-dimensional structures solved by X-ray crystallography has increased dramatically. By 2014, it had crossed the landmark of 100 000 biomolecular structures deposited in the Protein Data Bank. This tremendous increase in successfully crystallized proteins is primarily owing to improvements in cloning strategies, the automation of the crystallization process and new innovative approaches to monitor crystallization. However, these improvements are mainly restricted to soluble proteins, while the crystallization and structural analysis of membrane proteins or proteins that undergo major post-translational modifications remains challenging. In addition, the need for relatively large crystals for conventional X-ray crystallography usually prevents the analysis of dynamic processes within cells. Thus, the advent of high-brilliance synchrotron and X-ray free-electron laser (XFEL) sources and the establishment of serial crystallography (SFX) have opened new avenues in structural analysis using crystals that were formerly unusable. The successful structure elucidation of cathepsin B, accomplished by the use of microcrystals obtained by in vivo crystallization in baculovirus-infected Sf9 insect cells, clearly proved that crystals grown intracellularly are very well suited for X-ray analysis. Here, methods by which in vivo crystals can be obtained, isolated and used for structural analysis by novel highly brilliant XFEL and synchrotron-radiation sources are summarized and discussed.